Typically the performance issues are just that Spotlight reindexes the drive after the install. This can slow things down quite a bit for a few hours or days, depending on various factors.

As for the trackpad issue, first try resetting the PRAM. A number of trackpad related settings are stored there, and sometimes they kind of fight with plist files.

You should also forget that ~/Library even exists, and the same with /Library. Apple made them hidden folders by default in Lion for a reason. They're sort of like the Windows Registry. Probably 99.999999% of us should forget that we ever knew about them. Go messing around in there without knowing EXACTLY what you're doing, and you will almost certainly create a few additional problems whether or not you resolve the initial one. There is almost never a good reason for anyone, even we experts, to be spelunking around in a Library folder.

Still, I'm wondering why the person at the Apple store didn't resolve your trackpad issue as well since you were there. Of course it's entirely possible their earlier actions are what caused it in the first place. From your description, it sounds like the person was just using a shotgun approach to troubleshooting: Do a bunch of different things and see what sticks.