So Eliza,
Im guessing that you followed the install instructions to a T ?, that being long thread to bottom case and short thread to top then tensioned to a max of 8ft/libs. That is the normal way and it is not unusual for the studs to be at different heights, combined with the extra tall heavy duty nuts which makes it look nuts. BUT it is OK. re pretensioning, a few heat cycles is all it takes then retention.
Now the best way !
Install the studs with a dab of lock tight on bottom and install so they are at the height you want and all the same ( except for the two short studs)
Let them dry for a couple of days then or even better while loctite is wet place on barrel and head , lightly tension the head nuts evenly to stabilise the studs angles and position , then let dry for couple of days.
Then after assembling engine etc normal tensioning to 22 ft/lbs, leave for a day then retension several times until no more creep on the nuts/stud.
If you do this multiple pretensioning until no nut creeping it saves doing a hottest and removing engine etc,
Relax Eliza