Solution to #1:
Before installing your APR bar, did you wipe down the area where the plates will be sitting? Often times if that area is not smooth from debris, the plates will not sit 100% flat no matter how much you tighten - because there will be small grit/sand between the two flat spaces, making it possable for the plates to slide enough to make that knocking sound you hear.
Simply follow the suggestion that was already posted above and while you're at it, take a damp cloth and wipe down the areas of where the plates make contact to your vehicle.
From...INSTALL GUIDES >> SUSPENSION Installation Guides >> APR Flex Control Bar / Upper-Strut Tie Bar https://www.celicahobby.com/ubbthreads/thread.f0_57367_0_collapsed_5__1.html
I had similar problems with noise coming from the bar after installation, and it wasn't from it hitting the engine bay either. The solution I found on another site (and it seems to have done the trick), is to unbolt the bar and apply grease/lubricant to the bottom of the strut bar plates, as well as the rubber contacts on the top of the strut tower.
Seems that when taking turns or bumps, the rubber expands just a little bit, causing slight noise when it rubs against the metal plates. Minimizing this friction should eliminate the rubbing/grinding noises you hear.