I am very close to doing this now ... Yes 3 years later but I have taken care of other priorities, have more experience after swapping engines in my Jeep, and work is picking up so I have the extra cash to do it
The basic plan now is to take the entire 4.9 engine from a 91-93, plug the MPFI injector holes, and then put the 4.1 TBI throttle body and distributor on the 4.9 intake.
The 4.1 throttle body lets me keep the ports and linkages that I already have, without having to worry about things like cruise control or whatever. However the throttle body will have to be bored out to support the 4.9 airflow requirements and I will have to put Chevy 305 injectors in the TBI to get the fuel rates to match the increased displacement. There is a pretty good pool of experience in the Chevy performance world with doing 305 to 350 conversions and this approach is pretty similar to that, so I'm not particularly worried about this part of it. Actually it's easier for me since I only need to worry about air/fuel/spark which is all right there, and they have to worry about ESC controls and engine sensors that my Cadillac doesn't have. I may get a wideband O2 with an AFR gauge to watch air-fuel ratio but I don't think it will be necessary.
For spark, it looks like the 4.1 and 4.9 distributors have the same profile, so I should be able to install a 4.1 distributor in the 4.9 and be done with it. Here are pics from A1-Cardone showing 4.1 (left) and 4.9 (right) and the profile seems identical
The 4.9 added a cam sensor to the distributor but my 4.1 ECM can't use it, and swapping in a 4.1 dizzy will delete it so it's non-issue. The 4.9 also added a knock sensor but my 4.1 ECM doesn't know about that so I will just plug off the hole and forget about it. All of the other engine controls will stay with the 4.1 where possible (such as TPS, coil, etc), and a lot of them are the same anyway (coolant temp, oil pressure, etc.). Assuming the bosses on the intake are basically the same, I will keep my existing accessories. I may switch to the 4.9 power steering if it still on the engine but I will almost certainly have to plumb new steering lines for that and I'd like to minimize that kind of change. The AIR/smog pump seems to have been deleted from the 4.9 so I will have to do some mods there--I may have to add a resistor to the harness to fake out the valve sensor and keep the check-engine light from coming on.
One open question right now is how I will block off the MPFI injector holes in the 4.9 intake manifold. Since the only real force is the vacuum draw, I suspect that some basic rubber stopper plugs would work fine (rubber O-rings work for the injectors...) however I don't like the idea of parts being able to vibrate loose so I am also thinking about JB Weld or some other kind of semi-permanent solution.
Exhaust is also an open question. I looked at some trademotion catalog pictures and it seems that the 91-93 4.9 used the same exhaust manifold as the 4.5 engine, and since my 85 is the same C-Body as the 4.5 and early 4.9 then I should be good there. I will probably be able to keep my 4.1 exhaust from the cat converter back but I assume I will need the 4.5/4.9 manifold if my donor doesn't come with the setup. Since the AIR/smog will be deleted, I will have to plug off the side port on the cat converter. I may use the EGR valve from the 4.9 to allow for changes in exhaust pressure.