Yes, like Randy I'd like to know what the holes are for. I have removed and refitted the ZF in my car many times without removing the motor and only occasionally had any trouble. I do take care in lining up the clutch well, if I've had that out too, but it's only ever been spigot alignment that's cost me any time and frustration, apart from once after a lot of swearing I found the clutch plate splines were never going to slide on the input shaft. When using the clutch alignment tool I find it helps to raise it a little as you tighten the pressure plate. This is because the tool is able to droop a little through tolerances in the spigot bearing and clutch plate etc. I remember the first time I took the ZF out I removed all the header pipes and this took a long time.Since then I've found it unnecessary thank goodness for that. Hope you master it without taking the motor out Bill.
Ross