You mean the fan rotor won't fit? How does it not fit, as in it's tight and not wanting to go in?
I just did this swap a while ago, and the stock 5.9 E-fan rotor was a direct fit on the VDO/Siemens PM9069 motor. Rotor will only fit one way to the axle/ star- thingy, and it is a snug fit. So is the spring- loaded clamp that goes to the groove at the end of the axle when the rotor is fully pressed in on the axle.
Could you take a few pictures (clear ones, please) to show what's wrong. I've seen this swap now on a couple different forums, and not one has mentioned any issues with the fitment. If yours really isn't working with the VDO PM9069, then you might've gotten a wrong/ bad motor. It should be a direct fit in every possible way except for the additional pigtail you already bought.
1998 Grand Cherokee 5.9 LX daily driver, 1.75" BB, 32" KM2s, HPD30 Eaton e-locker/D44a stock LSD, 4.56 gears, custom- fabbed tube bumpers and tube fenders,...
1990 XJ Limited (4-door), 4.0 I6, AW4, NP242, ***rolled and totalled @ 165k miles***
1990 XJ (4-door), 4.0 I6, AW4, NP242, PBR 42" tires, Unimog 404 portal axles, 110" WB, full cage + uniframe completely rebuilt, front 3-link + panhard / double triangulated 4-link rear,... ***SOLD***