I recomend the pioneer deh x6500bt it has front usb for ipod/thumb drive, cd and bluetooth for hands free calling and audio streaming such as pandora I have installed at least 30 of them and have no problems yet ..they go for about 120-130 at best buy...
why not go with the cvrs again? but yea between the alpine and re I would def go with the type r ...re makes good stuff but the type r is proven and at that price not bad at all....also Kreepin I think he said its a crew cab
im assuming your locks still work off the door switch right? also ive taken many old remotes apart and look for old cracked solders that can loose contact
also consider the acouistics of the material even if a box made of cardboard were sealed air tight it would not sound good due to its density and resonance