If you only need the two newest achievements added on 16/05/22, you can get these by skipping to the "Combination Checklist" part of this guide, as these achievements are not retroactive. If you are playing for the first time, you can use this guide as normal and everything should unlock fine.

The game doesn't do the best job of explaining the controls, so I'll cover these briefly.

WASD or Arrow Keys - Moving your "cursor" yellow square around the grid.
E - Opens menu, used for using, examining and combining items.
F - Picks up or drops an item.
Alt - Rotates an item you are holding.
P - Resets the puzzle. Word of warning, this has no confirmation.
Esc - "Backing out" of an action - i.e. if you accidentally try to combine something and you want to stop trying to combine it? Escape.
Q - Can quickly switch between the two grids

Update - As of 16/05/22, Mouse controls have been added and keys can be rebound now so this is mostly unimportant.

There are two achievements where you may want to track items for, which are "Can I eat that?", for using every health item, and "Did you catch the reference?", for examining every item. If you want to copy this list somewhere and tick off which you use/examine as you do so, you may save yourself some time.

• First Aid Spray
  
• Brown Egg
  
• Green Egg
  
• Sardine
  
• Rotten Sardine
  
• Green Herb
  
• Herbs Vial (G+G)
  
• Herbs Vial (G+G+G)
  
• Herbs Vial (G+R)
  
• Herbs Vial (G+Y)
  
• Herbs Vial (G+R+Y)

• Handgun
  
• Shotgun
  
• Rocket Launcher
  
• DMP
  
• Riotgun
  
• NK-13
  
• Killer6
  
• Fixed Butterfly
  
• Dlaser-935

• HG Ammo
  
• SG Ammo
  
• MP Ammo
  
• MG Ammo
  
• RF Ammo

• Blue Gunpowder
  
• Red Gunpowder
  
• Green Gunpowder
  
• Red Smoke Grenade
  
• Green Smoke Grenade
  
• Yellow Smoke Grenade
  
• Red Herb
  
• Yellow Herb
  
• Herbs Vial (R + Y)

You may not encounter all of these items through natural gameplay, which is why I recommend using this as a checklist so that you can revisit after completing to examine/use the ones you missed. You will most likely miss Herbs Vial (G + G) and Herbs Vial (G + G + G) if following this guide to the letter.

On 16/05/22, 2 achievements were added: "It's just basic chemistry, yo" and "Master Stacker" - The first requiring all ammo to be crafted, and the second for combining every item that can be combined. This is a checklist of all item combinations and should be enough to get you these two achievements.
Combining two stacks of the same ammunition is part of this.

Blue Gunpowder + Blue Gunpowder
Red Gunpowder + Red Gunpowder
Blue Gunpowder + Green Gunpowder
Green Gunpowder + Green Gunpowder
Green Gunpowder + Red Gunpowder

HG Ammo + HG Ammo
SG Ammo + SG Ammo
MP Ammo + MP Ammo
MG Ammo + MG Ammo
RF Ammo + RF Ammo

Green Herb + Green Herb
Herbs Vial (G+G) + Green Herb
Green Herb + Red Herb
Green Herb + Yellow Herb
Red Herb + Yellow Herb
Herbs Vial (G+R) + Yellow Herb
Herbs Vial (G+Y) + Red Herb
Herbs Vial (R + Y) + Green Herb

Handgun + HG Ammo
Shotgun + SG Ammo
DMP + MP Ammo
Riotgun + SG Ammo
NK-13 + RF Ammo
Killer6 + MG Ammo
Fixed Butterfly + MG Ammo
Dlaser-935 + RF Ammo

The images represent what needs to be in the "inventory" to complete it. This is all assuming that you reload your guns appropriately, and heal when appropriate too.

Later on, there are levels where you can fail a level by combining the wrong item, by using an item in the wrong order, by using the wrong item, or even by reloading guns in the wrong order. I will try to point this out whenever it happens. If I don't mention it, it is probably safe to assume that it is fine to stack ammo, heal, and reload as appropriate.

After examining the gun, you should have the "Stranger, now that's a weapon!" achievement.

Filling out the level this way should unlock the "You're not ready yet!" achievement. After you get this, reload the guns and you should then get the "Magic Pockets" achievement and be able to continue to the next level.

Filling the level out this way first should unlock the "Not enough health, Stranger" achievement. After you get this, use the First Aid Spray and you should get the "First Aid" achievement and be able to continue to the next level.

Combine the two Green Herbs into Herbs Vial (G+G), then use this to heal. This should get you the "Chamber's pupil" achievement. Remember to examine the item to save time later!

Attempt to use the Red Herb from the menu. This should unlock the "Wait, that's illegal" achievement. After this, you can combine it with the Green Herb to make Herbs Vial (G + R), and use this to heal.

• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.

• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.

• Use one of the Green Herbs.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.

• Eat the Rotten Sardine to unlock the "Intoxicating Power" achievement.
  
• Use the regular Sardine to heal.

• Eat both Green Eggs.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.

• Eat one Green Egg.
  
• Use a Green Herb to heal.
  
• Eat the other Green Egg.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.

• Eat Rotten Sardine.
  
• Use First Aid Spray to heal.
  
• Eat Rotten Sardine.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.

• Eat Rotten Egg.
  
• Use Green Herb to heal.
  
• Eat Rotten Egg.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.

• Combine Red and Red Gunpowder.
  
• Combine Blue and Blue Gunpowder.
  
• Reload Guns

• Combine Red and Red Gunpowder.
  
• Combine Blue and Blue Gunpowder.
  
• Combine Green and Green Gunpowder.
  
• Reload guns.

• Combine Blue and Green Gunpowder.
  
• Combine Green and Green Gunpowder.
  
• Reload guns.

• Combine Red and Green Gunpowder
  
• Combine Red and Red Gunpowder
  
• Combine Blue and Blue Gunpowder.
  
• Reload guns.

• Combine Red and Green Gunpowder.
  
• Combine Blue and Green Gunpowder.
  
• Combine Red and Red Gunpowder.
  
• Combine Blue and Blue Gunpowder.
  
• Combine Green and Green Gunpowder.
  
• Reload guns.

• Eat Sardine to heal.
  
• Combine Red and Green Herbs.
  
• Use Herbs Vial (G + R) to heal.
  
• Combine Red and Red Gunpowder.
  
• Combine Blue and Blue Gunpowder.
  
• Combine Green and Green Gunpowder.
  
• Reload guns.

• Eat Brown Egg.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.
  
• Combine Green and Green Gunpowder.
  
• Combine Red and Green Gunpowder.
  
• Combine Blue and Blue Gunpowder.
  
• Reload Shotgun first.
  
• Reload other guns.

• Use Green Herb to heal.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.
  
• Combine Red and Red Gunpowder.
  
• Combine Red and Green Gunpowder.
  
• Combine Blue and Blue Gunpowder.
  
• Combine Blue and Blue Gunpowder.
  
• Reload guns.

• Use Green Herb to heal.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.
  
• Combine Red and Green Gunpowder.
  
• Combine Red and Red Gunpowder.
  
• Combine Green and Green Gunpowder.
  
• Reload Fixed Butterfly first.
  
• Reload other guns.

• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Combine Red and Red Gunpowder.
  
• Combine Red and Green Gunpowder.
  
• Combine Green and Blue Gunpowder.
  
• Reload Fixed Butterfly first.
  
• Reload other guns.

• Eat Rotten Sardine.
  
• Eat Sardine to heal.
  
• Combine Green and Green Gunpowder.
  
• Combine Red and Red Gunpowder.
  
• Combine Red and Green Gunpowder.
  
• Combine Green and Blue Gunpowder.
  
• Reload Fixed Butterfly first.
  
• Reload other guns.

• Eat Green Egg.
  
• Use First Aid Spray.
  
• Eat Green Egg.
  
• Use First Aid Spray.
  
• Combine Blue and Blue Gunpowder.
  
• Combine Red and Green Gunpowder.
  
• Combine Red and Red Gunpowder.
  
• Reload guns.

• Eat Rotten Sardine.
  
• Eat Sardine to heal.
  
• Combine Red and Green Herbs.
  
• Combine Red and Red Gunpowder.
  
• Combine Red and Green Gunpowder.
  
• Combine Green and Blue Gunpowder.
  
• Combine Green and Green Gunpowder.
  
• Combine Blue and Blue Gunpowder.
  
• Reload guns.

• Eat Green Egg.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.
  
• Eat Green Egg.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.
  
• Combine Red and Yellow Herbs.
  
• Combine Blue and Blue Gunpowder.
  
• Combine Blue and Blue Gunpowder.
  
• Combine Green and Green Gunpowder.
  
• Combine Red and Green Gunpowder.
  
• Reload Shotgun.
  
• Reload Fixed Butterfly.
  
• Reload other guns.

• Eat Green Egg.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.
  
• Eat Green Egg.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.
  
• Use Herbs Vial (G + R + Y) to heal.
  
• Combine Red and Yellow Herbs.
  
• Combine Herbs Vial (R + Y) with Green Herb.

You should now have unlocked all achievements for level completion and most other miscellaneous achievements. If you are still missing the two achievements for examining all items and using all health items, you can reopen a level and make the items you need to eat/examine. Level 40 is a good one for this as it has a lot of herbs. Hopefully, you followed my advice on using the checklist and this shouldn't be an issue.