Most people will agree that the best way to build a 4 mill stroker is to run domes cut for the stroker crank, and no spacer plate, and have it ported for the 4 mill with cut domes.
A 4 mill stroker crank allows the piston to drop 2mm farther down in to the jug (BDC) and it aslo pops out of the jug 2mm (TDC). That is why your domes are machined 2mm for for the stroker crank.
You can check this clearance. Put the motor together with no spacer plate and your cut domes. Bend a pice of Solder in the shape of an L, Stick it down through the plug hole so it touches the side of the cylinder. Roll the motor over by hand with the kicker. It will smash the solder. Then measure the solder's thickness where it was smashed. Most people shoot for .035-.040. When you stick the solder in to the cylinder make sure you go parallel with the wrist pin. If you do it over by the exhaust port or intake port the piston could rock a little in the bore causing an inaccurate reading.
As for the port timing. When you run no spacer plate with no porting the piston is still going to go 2mm down past the ports. Add that 2mm spacer plate in there now the piston is going to be going down 4mm past the ports.
The 2mm spacer plate will advance the timing of the exahust port. A raised exhaust port does help top end power. If you ran no spacer plate it will lower the exhaust port, giving better bottom end. I would run no plate. That way all the stock porting is working together. I however wouldnt plan on keeping it this way. I would get the jugs ported. It will run fine with no problems not being ported. It just wouldnt run as hard as it could. Same is also true for a stock ported, stock stroke banshee.
josh