Unsolicited update on my mostly blind Paradox run, at roughly ~60 hours
Without spoiling anything some quick notes/answers to what you were wondering:
1) Monsters sharing affinity is strictly gameplay. I think it's ripping off some other monster collector games (SMT??).
2) You may as well spend money whenever you want to. There's some easy enough tricks to generate oodles of money so you'll never really be stuck by not having money but you might potentially be stuck by not having good gear.
3) You should definitely swap out Lime. The game has so many little interactions and even the most generic monsters get at least one or two. I know the natural instinct is always to use the main characters but I feel like you are missing out on a lot of the fun of the game that way.
4) The plot roughly follows the original VN but the moment to moment segments are all very twisted and weird (most obviously, humans and monster girls did not really get along at all except with rare exceptions and in the post game). The original VN was a good story, maybe not terribly special but much higher quality than I would expect from an h-game. Paradox's writing is incredible - it isn't perfect, mind you, but it is deeply engaging and fun to read throughout.