I hate to speculate where the problem lies, but here are two certain facts...
I've had a engine in and out of this vehicle numerous times for various reasons since I began this project last year and never once had any difficulty inserting motor mount bolts.
I don't recall ever putting a tape to it either before I began or during this project before the roll bar install. Considering all the time I have spent in and around this vehicle the past twelve months I find it hard to believe I would not have noticed a peculiar lean towards one side. Not one to rely on my oft feeble memory alone...I have a considerable amount of camera images that do not reveal any such lean.