The first thing you need to do is single out the problem. Posting a vague description of "he doesn't feel the difference in power at all" really doesn't mean much to me or perhaps anyone on here. There could be alot of factors. Find out if VTEC itself is actually engaging. If it's not, there is your problem.

As far as the transmission goes, well let me say the stock ITR transmission isn't exactly the beefiest transmission on the market. Unexperienced shifting and time eventually lead to the pre-mature wear and tear on the synchronizers inside the transmission. This is most noticeable with the infamous grind. The winding problem may be a bearing inside the transmission. An there are numerous bearings inside the transmission that may cause it to whine. Make sure the whine is coming from the transmission before you go inside of it though. It could be something else. Differential shims wearing may cause a whine in the transmission also.