you shouldn't need a new alt for an sax1200, i know i didn't need one for my sae1200. be weary of the prefab boxes, more often than not the cubic foot they post for the box specs are a bit inflated. so in other words, don't get some subs that max out at that cubic foot. for budget amps i would look into soundstream (rubicon and stealth series). you can find some good deals on amps if you look right; i know woofersect had some cadence amps for only around 250 that originally sold for 400+. and sundown is by far a good choice, i got my sae1200d v.2 at dbr.com for around 320 shipped and it was a referb, i've yet to have problems with it. though you should note that the sundown amps are underrated and my sae1200 truelly puts out over 1500wrms with no problems.
as for your speakers i would look into some custom ways to mount them to the door panels. speakers on the dash is a 100% enemy of sound quality, you don't want your sound signal playing at the windshield like that, the glass reproduces harsh sounds.
what's your budget for everything? including wiring and other misc. parts