1. Uhhhhhh I didn't replace anything. Miltank doesn't learn anything at level 45 in the base game, and in fact doesn't learn Refresh in ANY game at all. Are you thinking of Heal Bell? (which is still in its level up learnset at 48, I did not change that)
2. Noted!
3. Weird but idk how to fix that, and as you say it's probably not a priority.
4. I genuinely do not remember, do the base Unown forms exhibit this behavior too? (ie if you recruit a J, then the Q will turn yellow too for example?)
5. again, I can't do that without removing existing exclusive items, and that's kinda against my M.O.
word of warning, you cannot recruit everything, the base game's recruit limit of 552 is still in effect. I would be interested to see the spreadsheet when you're done though! ^^