You would have to get the OBD II processor, wiring for all the new sensors, all the sensors. Everything else should bolt up. You might also need to upgrade the evaporative emissions system so you don't get a check engine light (wouldn't be too hard).
....If i were you, this is what i would do:
since your intake manifold and cylinder heads fully ported/worked over - flow better than the newer split port cylinder heads and intake manifold (also ported) I would probably just buy another 3.8L engine from your year or use your engine, get a better camshaft, port and maybe extrude hone the cylinder heads and intake manifold, intall larger valves and mill the cylinder heads, buy a larger throttle body, MAF sensor and get Cold air induction and better (dual) exhaust and you'd have one powerful 3.8L.
There's alot of 3.8L performance engine building shops/companies out there so you can easily build up your existing engine.
You could also buy the bottom end of a F-150 V6, which is a 4.2L and is a cheap stroker kit (low mileage bottom end, or rebuild a 4.2L bottom end).
Good luck,
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2005 Suzuki Hayabusa GSX1300-R
1980 Ford Thunderbird - 255 V8
ported heads, 5.0L ported stock headers, O.R. H-pipe and Flowmaster 2-chambers, dual roller timing chain
hi-po Mack Truck hood emblem
1985 Mustang GT 5.0L T5, F-303, GT40p, headers, off-road h, flowmasters, MSD stuff, etc.
Sold 02/06/04 
1989 Mustang GT ET: 13.304@102.29 mph (5-24-03)
Sold - 1998 Mustang Cobra coupe, 1/4 mile - street tires: 13.843@103.41 (bone stock)
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