Well, you can hear a 'pop' or mild 'bang' when you shift into the small chainring, since you're letting the tension out of the cable in one go. I don't know if it's different than what you had before. As for a 'crunch' noise, that seems quite odd. You're not shifting under load, are you? Sorry if I can't help any more, maybe this bump will get someone's attention.
As for the top gear on your RD (I assume you mean the smallest cog), there's no reason in principle why it shouldn't work with the components you have. When it doesn't work are you are using your small ring up front and the small cog in back? That may cause trouble - there may be a trade-off between removing cage-rub from the FD and getting your smallest chainring to cooperate with your small cog (which you probably don't need to use anyway). Perhaps the more experienced BF minds can help out. At any rate, there is a basic run-through on how to adjust indexing at http://www.parktool.com/repair/readhowto.asp?id=64 and it's non-destructive (see also the links to other adjustments).
i ended up taking it to my LBS. A little lube and a little tweak in the tension and it seems to be ok now. Good thing I took it in, my crank was a bit loose and i was a getting a little creak they were able to fix up.
as for the RD, i was never cross chaining and a little adjustment took care of the problem. i really need to learn how to make these small adjustments myself...