Yes
I don't know what will happen with your needles though, It will want tuning.
The big difference with the EFi lump is the heads are slightly better, the combustion chamber is different and the valves are bigger. Also the exhaust manifolds are much better but I think the driver's side one will not fit if memeory serves correctly. The 3.9 also had a much better cam than the 3.5 and this accounts for the extra HP that the 3.9 had.
If you fit a 3.5 you can still add the 3.9 cam.