For your reference mate, the stock stud lengths are
Long Stud - 195mm OAL
Short stud - 160mm OAL
Installed height
Long Stud - 170mm
Short Stud - 130mm
First image shows stock studs on APE HD studs for comparison
Second shows the stock stunds installed - 170mm and 130mm height from top of case.
The best thing to do now is to Loctite the studs into the case and set the heights (above) as evenly as you can.
It doesn't have to be a micro measurement, just get them as close as you can by eye with a steel ruler.
The warning here is, don't flood the stud threads with Loctite.
Lightly coat the threads in the case with a toothpick and then screw the studs into the case.
Reasons being that too much liquid runs the risk of "hydraulicing" the stud in the threaded hole and secondly and most importantly, there's every chance that the oil galleries that let oil feed the top end will be blocked solid.
If that happens, you'll be pissed off big time.