OK, now I know how the Doc just loves these gearboxes
Check the roll pins in the linkages are in good condition and the sleave that they go in to. Also check the rubber bush on the back of the diff housing is in good nick too. I've seen some shifters that have worn bushes on the shift rods and these do make for a sloppy shift.
It sounds like you may have the plate on the bottom of the shifter in back to front (hence why you need to lift the stick).
Check that the cotton reel mounts are good and that the brackets are not bent, then with it all bolted up, undo the 1/2" UNF Nut on top of the shifter body that is on the steady and then do it up again, holding the shifter body so that it doesn't cock over to one side.
It would also be a good idea to check one (or both) of your engine mounts and / or steadys aren't broken.
These are a good shifter mechanism, but like anything else, if it has worn or mis-aligned parts it will give trouble. I have the Mini Spares short shifter in a couple of my own Minis and I think they are great, however if the mech is worn or mis-aligned I think they'd be rather horrible.
<EDIT> I'm pretty sure that 'converting back' from the short shifter would also give trouble as the holes for the locataing pins (for the shifter and the cap) will no longer hold the pins in place.