In chapter one I forgot to do the one acorn quest with the faeries and there is not much I can do about that now since Im way past that and you cant get back into that dungeon. My question is can you do quests for other chapters if you can still get there?

you can do any side-quests during any chapter you have access to the place you need to go. you can deliver the acorns to the dryads anytime. if you didn't get the acorns from the dungeon then i guess you'll have to use the item list to get them.

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trux

Probably a spoiler
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Im pretty sure that once your out of Irenicus' dungeon all the quests are available at any time (except the stronghold quests for classes other than your own)

Also if you give Bodhi the money before doing the tasks for Renal Bloodscalp, then Renal will be gone.

There are probably other quests which come available/unavailable as you take your path through the game.