Well, it's hard to give straight answer without really seeing your set-up.
The first question is - why a 4 - channel amp? Are you only currently running 2 of the 4 or bridged or ?
Not really sure on this one. All of the components were there when I bought the car from its second owner. The first owner put them in so I don't know if he bridged or what. No sound from the middle speaker (assuming its still there - just from the door speakers. There is also no factory footwell sub speaker anymore.
What is your bandpass set to on the amp - is it set for full-range? It should be, if you are not running a sub. This is an easy place to lose low-end, if it's set to high-pass with the frequency dial set to cut off the bottom. Check that first!
Great first start! I will check these settings when I can figure out how to remove what looks like a protective piece covering all of the controls on the amp. The CD Changer is mounted right in front of the amp so room is limited. It also doesn't help that my struts won't hld up the trunk lid and it keeps falling on my head as I poke around (that one is an easy fix though!)
The head settings should be similar - have to make sure that you aren't cutting off the bottom - are you sure the head is 634? Doesn't sound like a typical Alpine H/U designation although does fit the Changer .....
If it has control to select sub, set to 'off' and ensure if there are any frequency compensations or equalizations, you set them properly.
You won't get great bass from 5.25" but I think it must still be capable of better than what you are describing. One thing that helps in bass response is to stiffen your doors with 'mat & seal all the openings in the door face. A quality set of 6.5's will yield better results at the low end than the 5's but if you have a fundamental problem with what frequency is getting to them, won't fix your problem. What model Eclipse are they? Are they components? I know that one local guy has the Eclipse 6.5 components with no sub & it sounds pretty good!