Don't mean to make you sway from this swap but, you have an engine that when built right could handle a ton of power, then with a t-trim you could easily make over 7-800rwhp. So why bother swapping to an engine that could make the same power with a more modification than what you could spend on making your engine a beast. Let's do some figures, you could get a first gen for around 1500+ 1500 for the computer, because you cannot use yours, 900 for exhaust for BBK headers and x-pipe, 1500 for the other companies. Then minimum 2500 for supercharger bracket, then 800 for pbh accessories bracket. So your looking at roughly 7-8k for a coyote swap. I could build one wicked first gen. mod motor and up grade to a tko or t56 transmission for that...
But if you still thinking about the coyote swap here's a run down on your questions you asked.
First, yes you can use the bell housing and transmission with the coyote.
Second, you wold have to get a hole new supercharger bracket and plumbing. The reason, the coyote timing cover is totally different from that of the first gen mod motor. And, the reason for the piping, is location is different as well.it is no longer mounted reverse, most centerfug. superchargers are located off to the side like that of the pushrod motors.
Third, there are three manufacturers that make long tube headers and x-pipes. Just look for the ones listed for 79'-04'. You will have to run a tubular k-member on all of them. As for the factory headers, you could modify them and then possibly use a modified shorty header h/x- pipe setup. Look up some information for coyote swap for fox body, since they are basically the same vehicle and you can get an idea. Sean hyland used the factory headers on a swap and it was documented in a couple magazines.