Your not gonna want to mold your whole stock dash like that. If something under you dash goes bad, you wont be able to remove it.
It is possible to make a pod for speakers and not have to smooth out the wholes door. You mask the door panel and build a glassed base on the panel. Then use the mold youve made to build a pod. The pod will have to secure to the door somehow after. Somthing like this:
http://www.diyautomods.com/forum/showthread.php?p=55