So I've made a few alterations to the guide as I've said in the comments. It seems I had put the save in the wrong place for Gekkamaru and Chojiro and this was stopping the Chapter 5 memoir from unlocking.
Now you should save before the choice in Chapter 5, because choosing the answer that gives no affection will get you the memoir (Thanks Linhette ♥ for pointing this out!)
This would make sense as to why the other 3 guys memoirs completed just fine, but there's been problems with the first 2 I played through... *sigh*
(Guide is up to date so you can just follow it without worrying where to save etc)

Anyway, hopefully it should now flow better and you should be getting a full gallery of CGS and memoirs (after viewing the guy's gallery the achievement will activate)

• I should talk to Gekkamaru (♥ Gekkamaru)
  
• I'm glad we get to work together
  
• You're leaving me here?
  
• Goro-san
  
• Keep Quiet (♥ Gekkamaru)
  
• Residential District
  
• I know you weren't (♥ Gekkamaru)
  
• Try to resist
  
• Bow deeply in silence (♥ Hanzo)
  
• Fushimi Castle, Main Gate
  
• Don't worry (♥ Gekkamaru)
  
• MAKE SAVE HERE
  
• You look very handsome (♥ Gekkamaru)
  
• Residential District + Main Street + Fushimi Castle, Main Gate (Fushimi Castle needs to be last, it doesn't matter which of the other 2 choices you pick as first and second)
  
• Of course. You're a great cook (♥Gekkamaru)
  
• No excuses (♥Gekkamaru)
  
• Hold his hand (♥Gekkamaru)
  
• Well... (♥Gekkamaru)
  
• Don't resist (♥Gekkamaru)

I just chose the opposite options from the answers above ^^

• (LOAD SAVE)
  
• Your movements are beautiful
  
• Fushimi Castle, Main Gate
  
• I'll eat as much as I can
  
• I understand
  
• Pat his futon
  
• It's nothing
  
• Resist

These answers will get you all of Gekkamaru's CGs, but I found that in order to make the achievement ping I had to go into Extras and view the gallery. Also I am missing one of his memoirs, I believe it's in Chapter 5 but I can't figure out how to get it yet.

• I should thank Brother Chōjirō (♥Chōjirō)
  
• I'm glad we get to work together
  
• All right (♥Chōjirō)
  
• Goro-san
  
• Keep quiet (♥ Gekkamaru)
  
• Main Street
  
• I'm sorry for how I behaved
  
• Try to resist
  
• Stand up for Brother Chōjirō (♥Chōjirō)
  
• Residential District
  
• (MAKE SAVE)
  
• That's not true (♥Chōjirō)
  
• Residential District + Main Street + Fushimi Castle, Main Gate (Fushimi Castle needs to be last, it doesn't matter which of the other 2 choices you pick as first and second)
  
• I wonder how everyone is doing (♥Chōjirō)
  
• Someone I truly respect (♥Chōjirō)
  
• I wanted to stay with him (♥Chōjirō)
  
• Attack (♥Chōjirō)
  
• Hug him (♥Chōjirō)
  
• You're right (♥Chōjirō)

• (LOAD SAVE)
  
• I never thought you would think that way
  
• Residential District + Main Street + Fushimi Castle, Main Gate
  
• What's going to happen to me?
  
• Someone I aspire to be
  
• I want to apologize to him
  
• Watch his movements
  
• Stroke his head
  
• You're wrong

These answers will get you all of Chōjirō's CGs, but I found that in order to make the achievement ping I had to go into Extras and view the gallery. Also I am missing one of his memoirs, I believe it's in Chapter 5 but I can't figure out how to get it yet.

• I should make preparations
  
• I'm so happy to see you after 8 years (♥ Kuroyuki)
  
• You're leaving me here?
  
• Goro-san
  
• Make an excuse for Kuroyuki (♥ Kuroyuki)
  
• Fushimi Castle, Main Gate
  
• Were you really joking? (♥ Kuroyuki)
  
• Try to resist
  
• Bow deeply in silence (♥ Hanzo)
  
• Residential District
  
• Because you get lonely easily (♥ Kuroyuki)
  
• I can't do that
  
• It was a coincidence
  
• But...
  
• (MAKE SAVE)
  
• Of course (♥ Kuroyuki)
  
• Residential District + Main Street + Fushimi Castle, Main Gate (this one last)
  
• Of course not (♥ Kuroyuki)
  
• Go outside (♥ Kuroyuki)
  
• All right (♥ Kuroyuki)
  
• I don't know (♥ Kuroyuki)

• (LOAD SAVE)
  
• Maybe
  
• Residential District + Main Street + Fushimi Castle, Main Gate (this one last)
  
• I was just amazed
  
• Wait
  
• I'll fight with you
  
• He's not.

These choices unlocked both of his endings and got me a full gallery of CGs and memoirs. Again you have to actually go into the Extras menu and view his gallery for the CG achievement to ping.

• I should make preparations
  
• I'm glad we get to work together
  
• You're leaving me here?
  
• Goro-san
  
• Make an excuse for Kuroyuki (♥ Kuroyuki)
  
• Fushimi Castle, Main Gate
  
• That's a relief (♥ Kuroyuki)
  
• Don't resist (♥ Hanzō)
  
• Bow deeply in silence (♥ Hanzō)
  
• Fushimi Castle, Main Gate
  
• I will do my best (♥ Hanzō)
  
• I can't do that
  
• It was a coincidence
  
• Understood (♥ Hanzō)
  
• (MAKE SAVE)
  
• Is Lord Takugawa receiving unexpected guests? (♥ Hanzō)
  
• Residential District + Main Street + Fushimi Castle, Main Gate
  
• How do I fight him? (♥ Hanzō)
  
• I should stay (♥ Hanzō)
  
• How many are there? (♥ Hanzō)
  
• All right (♥ Hanzō)
  
• Thank you for saving me (♥ Hanzō)
  
• I like it (♥ Hanzō)

• (LOAD SAVE)
  
• You're very knowledgable
  
• Residential District + Main Street + Fushimi Castle, Main Gate
  
• I can't win...
  
• I should go
  
• What should I do?
  
• I can't
  
• I'm all right
  
• It suits you

This should get you all CGS and memoirs. I checked after completing his Happy Ending and half of his memoirs were still missing, so you have to complete his bad ending to get them all.

Hanzō has been my favourite so far <3

• I should make preparations
  
• I'm glad we get to work together
  
• You're leaving me here?
  
• Goro (♥ Goemon)
  
• Keep quiet (♥ Hanzo)
  
• Main Street
  
• I've never had such good dessert (♥ Goemon)
  
• Try to resist
  
• Bow deeply in silence (♥ Hanzo)
  
• Bukemachi
  
• All right (♥ Goemon)
  
• I'm sorry (♥ Goemon)
  
• But...
  
• SAVE HERE
  
• I'm fine here (♥ Goemon)
  
• Residential District + Main Street + Fushimi Castle, Main Gate
  
• I don't think I can play a good wife (♥ Goemon)
  
• I feel shy (♥ Goemon)
  
• You'll make a wonderful husband (♥ Goemon)
  
• That doesn't change the fact it hurt (♥ Goemon)
  
• You're coming with me (♥ Goemon)
  
• Having you stroke my head (♥ Goemon)
  
• I believe we're destined (♥ Goemon)
  
• Meet his eyes (♥ Goemon)
  
• Is it really a painkiller? (♥ Goemon)

• LOAD SAVE
  
• Let's go to the dessert shop
  
• Residential District + Main Street + Fushimi Castle, Main Gate
  
• I don't think we'd be convincing
  
• Stop teasing me
  
• You'll be a good father
  
• Don't force yourself to laugh
  
• That's unlike you
  
• Sleeping in the same room with you
  
• I'll be waiting
  
• Look away
  
• Is it poison?

This should get you all memoirs and CGS.

NOTE:

The below guides might not work for you unless you have followed my previous guides to the letter. It looks like in order to unlock all memoirs you have to exhaust all possible choices/options in the game- and for those that have done part of the game without this guide you might have already picked from the options below in previous routes, therefore they won't work or you might already have the memoirs/ part of the options to qualify for that memoir.

There's not really anything I can do about that, it seems like it's going to be a case of going back through the game and picking options you haven't done before and thats about it. Sorry guys, I tried but these memoirs have fried my brain and I don't want to look at them anymore, you're on your own from here on out! (」ﾟﾛﾟ)｣NOOOooooo━


Following the routes above should get you all of the memoirs except for 2. It took me a while but I've found out how to get them. There's probably an easier way but this is how I did it and I know it works, so please bear with me.
Also by this point you should be able to skip through the text to get to the choices you need.

I had 2 memoirs left in the common route- chapter 2 and the one between chapter 3 infiltration and chapter 4 undercover (the memoir is called chapter 3- undercover). Following the answers below will grant you these 2 memoirs and then you will unlock the 'all memoirs complete achievement', the 'all achievements' achievement (lol) didn't pop up until I came out of the Extras menu and back onto the main screen!
So without further ado....

• I should make preparations
  
• I'm glad we got to work together
  
• All right
  
• Goro-san
  
• Keep quiet
  
• Residential District
  
• But, just in case... (this might be far enough but I didn't check until after the next 2 answers)
  
• Try to resist
  
• Stand up for Brother Chojiro

• I should make preparations
  
• I'm glad we get to work together
  
• You're leaving me here?
  
• Goro-san
  
• Make an excuse for Kuroyuki
  
• Fushimi Castle, Main Gate
  
• That's a relief
  
• Don't resist
  
• Bow deeply in silence
  
• Fushimi Castle, Main Gate
  
• Not at all

Someone cleverer and with more patience than me could probably make these fit into Chojiro's and Hanzo's routes but to be honest I didn't mess with them too much.

So there we go! That should be all of the achievements for Nightshade!!