1.Yes you can retain the factory dizzy and it will work fine. Just leave all the wiring in for the ignition components on the 3.2. That means the throttle switches, knock sensors and original ECU stay put. However the problems you are having may be caused by incorrect timing and this won't help you get your engine running correctly. (Actually a bigger PITA then removing it and replacing with EDIS)
2.For one trip to the junkyard with a pair of wire cutters and a lap around the Ford area you can have enough EDIS ends to do 10 sets of wires. Last set I made I cut off about 20 ends in a junk yard (cost $5). Then I practiced on several of the ends before I had the science of taking them apart and making the new Porsche end down to an art.
3.Mount the EDIS coil pack up as high as you can and then run the VR wires under it along the engine. So far no problems for me. Just make sure you shield the wire very well on the VR connector. I used all factory Ford wiring the entire way.
4. Leave as much of the factory wiring in tact as possible. All you will need for Megasquirt and EDIS is key on 12V for the ECU/EDIS controllers. The 3.2 already is injected so use all the factory wiring for the injector power, fuel pump relay and ignition power. This will make later wiring trouble shooting easier for you or a later owner.
Now here is another idea. I am not sure if someone has done this yet, but the 3.2 already has a hall based crank position sensor. I would bet you could run the distributor off a Bosch 139 coil driver (found on Volvos, BMWs and VWs in the 80s).
MS1/Extra Ignition Hardware Manual . You could control advance and retard just like EDIS with the stock coil and dizzy. I have done it on a few VW 16Vs and it works great.
Let me do a little research on the 139 coil driver option. That may be the ticket for a 3.2 for simplicity and maintaining a factory appearance.