You can do the 4v. Or the 5.4 Lightning swap is more power and 5 speed tranny. But being a truck engine it sits higher. You can basically swap any engine into this that you can any other 4.6 Stang. It had the same engine as the earlier 2v Mustangs and IIRC the trannys were the same too (probably different shift points etc). I'd be very interested in a SBF or maybe even a BBF dropped into one that's emissions exempt but too many cars plus that may be a nice amount of custom work if the motor mounts for those type of swaps into stangs aren't perfect. You've got a nice amount of engine bay room to work with if you go with a smaller sized engine (demension-wise that is) because of how fat the 4.6's were considering they're only 281CI. You can make a nice amount of power on the 4.6 2v throwing a turbo setup in there but it's going to take custom work and that'll cost an arm and leg if you don't do it yourself. But the 2v's at least can only take around 400rwhp before possibly running into problems. You can get more outta them but that's just running on borrowed time.
Transmissionwise anything you can get a bell housing that'll bolt to a 4.6 if you have the right parts. You need to make sure you have the right flywheel for the tranny your swapping in too. The panthers had 8 bolt flywheels IIRC and some trannys require 6 bolt ones I think? I think the Cobra Vics had the Cobra 4v and their tranny's swapped into the panthers but all that work was done by Roush IIRC.
Here's a small write up about the parts needed for a Mustang 5 speed (t-45) swap into one. Like I said most parts are able to be found in the junkyard.
dRock96Marquis' 5-speed t-45 swap page
Here's one for a newer Mustang 5 speed thats a whole writeup.
The official manual transmission swap - Crownvic.net