[Blas]

Yes, with the addition on the parking brake disk on the driveshaft, the standard bolts will be too short for proper thread engagement. Obviously right? - You've added a new plate here...
Also, you want the unthreaded section of the bolt to be almost the same length as the plates it goes thru (the original two flanges on the driveshaft and rear end AND the new disk plate) If the threaded section of the bolt extends too far into the hole, the bolts will loosen over time causing a catastrophic failure, not far from the "seat of your pants"...at speed....And the proper bolt strength is IMPARATIVE....built in washer...way stronger than grade 8...
Here is what I know....someone should verify this first....
"...drive shaft bolt part # N800594-S100 this is a Ford part number. These are the 12m x1.75 thread 12.9 hardness with a 12 point head, they come with a small amount of red lock tight on them." The bolts should be torqued to 83 ft lbs
Hope this helps.....