For amps. I don't know, you are really limiting yourself with a size thing. Did you check the size of the Alpine F450? Here are your requirements when shopping for amps...
1) Decent power for speakers and subwoofer (somewhere around 4x50 and 2x200 bridged would be my goal)
2) Decent crossover (80-250Hz variable with at least a 12db/octave slope)
3) Speaker-level inputs (saves money when connecting to factory system)
4) Good sound quality (100db S/N ratio or better for starters)
My top choices, assuming they fit would be the following:
http://www.mobilesq.com/store/product_info.php?cPath=26_46_49&products_id=76 (make sure to get the DVC 4ohm sub for this amp)
http://mobile.jlaudio.com/products_amps.php?amp_id=261
(make sure to get the DVC 2ohm sub for this amp)
http://www.crutchfield.com/S-wsPcax0kcK6/cgi-bin/Prodview.asp?c=3&g=120&I=500MRPF450&s=0&cc=01
(make sure to get the DVC 2ohm sub for this amp)
For small projects you can get fiberglassing supplies at Walmart in the automotive section (and brushes and mixing pans in the hardware section). However, you'll have to order the vinyl/carpet from SelectProducts or a similar online store because I have yet to find a local store that sells it.
In your case, I would take out the panel and find a way to use it as a mold. Without the panel in front of me I can't really step you through how to do it. If you don't ever plan to remove the box, you could simply glue the mdf ring to the panel and then fiberglass directly to the panel to stiffen it up and seal any holes there might be. When you are finished, you can place a bead of silicon around the edge and screw the other baffle to the ring to complete the seal.
As 1sty mentioned, the more work you can do outside the car, the better. Otherwise the fiberglass resin will stink up your interior and it could take months before the smell goes away.