I have PSB Silver i's on my 990 as well. The grills should come off (mine do), but it might require a little more force than you're expecting. I doubt they're damaged.

Your new amp is probably better capable of driving the PSBs than your old one. The Silver i's have very good bass extension for a modestly sized tower speaker. I ran without a sub for a few years with them and was not disappointed.

The thought that your room is a big contributor here is probably spot on. It might be time to start getting scientific about it.

Get a Radio Shack SPL meter and download and burn this test CD (http://www.realtraps.com/test-cd.htm). Follow the instructions on the site for doing a simple room analysis. This should give you some insight as to how your room is behaving in the low frequency spectrum.