Optimizing HT setup for Analog: Where to begin?

The problem most likely is you are using an AVR - at least that is my own experience. I spent good money going from a highly rated Denon AVR receiver to separate Mcintosh and Lexicon HT equipment, with various speaker changes, trying to get it. It was great for movies/surround sound, but neither ever sounded great in stereo, never had a great sound-stage. Switched it all out to stereo. If you need to keep the HT, I would suggest getting a high-quality integrated made for stereo with a HT by-pass, you will get the sound stage you are looking for in pure stereo. That is my costly experience. One cheaper suggestion, disconnect the center channel and hear/see what happens. 

Right. AVR is crap. All of them. That and the center channel speaker, plus whatever else you have in the middle, these are all death to imaging and stage depth. 

The good news is a good stereo integrated amp and two speakers is way better quality for way less money than three speakers. With only two you can afford some quality wire too. DIY wire is your second crappiest component. There just aren't any good DIY wires. Period! I have one right now someone sent me as proof I am wrong, that only proved how right I am.

Where you start almost doesn't even matter, but since the AVR is such a total piece of junk, that only serves as a reason to keep the center channel you don't need, I would start with a good integrated amp. If you can stretch to $3k the Raven Nighthawk is an outstanding amp good enough to serve you the rest of your life, or for sure be an anchor piece for a good ten years. What's your budget?

Get a dedicated 2 channel only integrated. You are wasting your time trying to make a HT amp sound good for 2 channel audio. They are purpose built multi channel devices and should remain in that realm.