Back in 2005, I upgraded my receiver to a newer one (a ~$450 Pioneer) that had auto calibration, which I'd never had before. It made a world of difference in my setup. The Pioneer sounded about the same as my older Yamaha without any EQ, but accounting for the room acoustics was a big improvement. You might want to consider getting one of the newer receivers with auto calibration in it to see if it helps. Buy from a place that will let you take it back if you don't like it, and you have no risk.
In 2007, I added an external amp. It made a big difference at loud listening levels, the levels at which my Pioneer couldn't supply the dynamic power needed to accurately reproduce the dynamics. At normal listening levels, it made no difference to me at all. Do you think that the clarity is good at lower listening levels, but not at higher ones? If so, your receiver might be underpowered for your needs.
As for bookshelf speakers all around, that's what I do.
I use two pairs of the same speakers for front and back, paired with a center channel and a sub.