Clutch and engine alignment?
The clutch assembly/bell/pinion should be aligned parallel to the mainshaft. Tilting the bell/pinion assembly causes unequal distribution of load between the maingear and clutch pinion and can result in premature gear wear. The clutch/shaft is running in the clutch bell and is supported on the bearings. Since those bearings are in the same bearing block that supports the bell pinion, if you tilt the bell, you tilt the clutch and vice versa. Optimum build technique for any drivetrain is never represented by tilting or canting an assembly to compensate misalignment elsewhere.
The gentleman who used the techniques that I suggested, Mike Goza, is a long time MA team pilot and FAI pilot who has a massive amount of experience with the gas model. Adjusting the holes as needed and then installing the bolts is adequate to fixture the engine. Due to the moment arm in play from the mounting holes on either side of the frames up to the level of the clutch, it generally takes very little material removal to accomplish the task of alignment. The rear mounting plate will additionally hold the engine from attempting to shift fore or aft unless the frame holes are way oversized. I'm not sure why you are having aligment issues. My gas model lined up without incident. That said, I have two identical Furys which each needed their own particular amount of motor mount shimming to create perfect alignment.
Should you choose to investigate other options for your problem, I'd suggest you call MA and see what they have to say. I don't know of any other obvious solution to your problem.
Ben Minor