[notnew]

I bought a 68 stang w/ a 200 in line but iI don't like the 200 what I want is a 4.6 or similar engine in it. However I don't know a single thing about how the computer system works. As a matter of fact I haven't done any late model swaps mostly old stuff ie 50s

 

[meatball]

You'll want to look here for a start; You've got some research to do - keep us posted.
http://www.modularfox.com/

 

[Monkey Boy]

It can be done but it's not easy or cheap. I've seen a 4-valve 4.6 in a 65 before but the engine is so wide that the strut towers had to be eliminated and a custom front suspension made for it. The engine compartment on the 68 is wider but I'm not sure if it is wide enough.

 

[BlueStreak03]

Honestly I would just get a late 5.0 and put in there. It's a narrower motor and should fir right in with minimal modifications.

 

[meatball]

How about something like this:
http://www.uniqueperformance.com/GT350SR-40th.aspx
http://www.uniqueperformance.com/GT350SR.aspx
http://www.uniqueperformance.com/performance.aspx