[kitcarbp]

Steve, the big block short input shaft for either the top loaders or the TREMECs are way shorter and obvious when measured compared to small block input shafts. Your issue sounds like something else.
Couple of basic things to start with.
Is there a machinging burr or step inside the pilot hole preventing the pilot bearing from seating all the way ?
The pilot bearing you are using, is it the solid type or are you using a more modern needle bearing type?
Have you compared your pilot bearing to others made for 428 FE's to make sure pilot the bearing is not mis-machined ?
Do you have the correct QT block plate thickness for the QT bell housing you are using? Speak to whoever sold you the QT BH to confirm this.
As an example (not FE) , my OEM block plate on a BB Ford (385 series motor)OEM bell housing is 0.070 inch thick, giving me a total distance from engine flange to BH trans face flange of 0.070+ 6.250 = 6.320" . I am using a TKO 600 with the short input shaft kit installed.

I am not familiar with FE crank pilot hole dimensions (others need to confirm).
1) Do 428 FE auto trans cranks and 428 FE manual trans cranks have different pilot hole dimensions (depth wise) that could be causing this?
3) Is it an aftermarket crank whereby the pilot hole may not be machined deep enough (to print)? In any case it sounds like you desire your pilot bearing to either sit a little deeper into the crank pliot hole, or you want a pilot bearing that is a little thinner to avoid the interference. If its the solid type I have heard of folks machining the thickness it to fit the crank pilot hole, but this is usually only required when doing engine/trans conversions from different manufacturers. I would avoid the spacer if you can and see if you can get the pilot bearing to seat further into the pilot hole.

EDIT
I just checked the QT website for both FE part numbers (RM-6056 and RM-6057) and both are listed as total height of 7.050" and the QT motor plates are listed as 0.125" thick, this would give you 7.175" with plate to the rear face of BH. You stated you measured "7.11" on the TKO face to input end. So I would bet it must be the pilot hole in crank, pilot bearing or its installation into said hole.

For ref here are the TREMEC specs, it shows 7.21 from trans face to input end on std (long) input shaft.


good luck