I would be VERY hesitant to place speakers in a headliner, or any place above eye level. I don't know how technical you want to get, but I could lay out a possible way to make it work and give you decent performance, but I doubt a prefab design would work.
Do you have a link so I could see the headliner? Maybe I missed it, but I'm having a hard time visualizing how that could be successful. If you are trying to raise the soundstage, simply moving to a set of component speakers up front and placing the tweeter on the A-pillar or even mounting in the upper part of the door would accomplish this without giving you a feeling that you are wearing an amplified helmet.
Another option on the subs is to use a smaller driver.
Using a pair of these:
http://goo.gl/VvGLj
Would make it easy to fit under a seat and you can always add more later if you need it louder. I've used them in desktop computer stereo builds. They aren't gonna dislodge your windshield with too much bass, but have decent output. Another option would be to find a buyout on 8" subwoofers and do a couple of those. Simple, low profile installation. If needed, I could even design a box for ya (I would need some measurements).
There are some decent performing low profile subs on the market. They tend to get a little pricey, but I've been wanting to try out this guy.
http://goo.gl/OYXra
As far as other gear like amps, go find a car audio forum and you'll be able to track down some used amps nice & cheap. There are a lot more to choose from now that are decent quality than even 10 years ago when there was a major difference between brands.