Hi, truely thorough build this. Excellent to see the commitment and build quality being invested into the car. Your rewards will be long service return.
Regarding the engine height and clearance to the cross-member, My only suggestion there would be to lower it using a combination or mounts/parts or modify your original mounts to drop the engine.. you only need several millimeters of clearance..beware, engine mounts do sag/settle over time.
Doing this in combination of a engine torque limiting device ( read: chain restrictor or wire cable restrictor ) mounted between the engine mount main fastner bolt through the x-member and directly above to the bolt hole in the engine number pad, does elliminate 90% of your excess engine roll. Combining this with locating the "contact" points in the transmission tunnel, use of a good size hammer and punch ( to stretch the trans tunnel steel ) can make some room for the trans to pop up and mayby provide you with the clearance you need.
Alternatively cut the xmember top and reprofile the clearance provided between the sump ...and cut the top out of the trans tunnel and put in a blister
My xmember mod - Prodominately done for high energy sump installations- ever tried getting a engine out with one on and no xmember mod ---need to drop the xmember from the body to drop the engine
http://members.dodo....bag/xmember.JPG