I'll start:
Maybe some stuff that no one would ever notice?
For me no wires/linkage thru the motor plate.
Turned down v/c studs so that covers slip on/off easy without grinding any aluminum on the studs - bottom 1/4" of stud original size so it still pilots properly.
Machined v/c nuts with integral washer flange.
Installed pem nuts on aluminum parts - less likely to strip than threading the aluminum - easier to replace than helicoils.
I machined Teflon inserts (totally hidden) for steering linkage - where the links drag thru the aluminum brackets.
Removed pickup from oil pump so it could never fall off.
Modified my 1 piece girdle so you can individually preload each cap.
Added seat belt hangers so you can get in without sitting on them (may sound silly, but I am really glad I did this one.)
I added a coupler on the fuel tank to make draining it easier - just snap on the hose.
Care to share some of YOURS?
? :-)