Yea, it has been my experience that not only must the shift lever be removed from the "stub", via loosening the pinch bolt, but the stub must also be removed from the box, in order for the box to readily clear the sheet-metal beneath the firewall.
The stub does not HAVE to be removed (no doubt it likely makes it a bit easier) - it does take some finesse with the engine hoist to clear the top of the trans tunnel at the firewall (helps to have two people too - I can remove an engine and tranny by myself but haven't yet figured out how to install one solo yet).
Move the engine hoist strap from the middle studs on the head to the second set - move forward one place - this helps tilt the engine and trans to clear the tunnel. •If you don't remove "stub" - Tape (duct tape) circular covers in place around the "stub" or they will fall off and dirt will fall into the opening.
By all means take the hood off and remove the radiator and take the engine/trans out over the front of the car. I saw a photo somewhere of a Spider engine and trans poised over the car with the hood on like it was ready to go back in - I don't know if it can be done with the hood on - but IMHO hoods and radiators are too valuable to risk being "bumped" with an engine.
Also, I have learned the hard way - make sure that the car and engine hoist (assuming hoist has wheels) is on level ground - even a slight slope can result in accidental "bumps" or "rubs" with the engine and transmission.
•You will encounter interference with the drag link (that rod between the steering and the idler arms).
The front of the bell housing will catch on the tie rod if it is not moved. Get a proper Alfa tie rod end removal tool (borrow one or buy one from Highwood Motors - they are fantastic) and pop one tie rod end out and swing the rod down and out of the way - this takes only a few seconds with the correct tool and it won't mess up the tie rod end.
This will not screw up your alignment - I usually undo drivers side - easier to get at in my cars.
I have also discovered it is much easier to remove transmission with engine if you leave the flex donut on the driveshaft. Remove the front section (mark front and rear) of the driveshaft with the donut - don't forget to use a big hose clamp to compress donut so it "slips" off the studs.
If you leave the donut on the transmission it really hangs up in the tunnel and sheet metal can damage donut. Put the nuts back on the ends of the three studs on the transmission yoke to avoid messing up threads if they contact tunnel on the way out.
IMHO leaving the donut on the trans and trying to line up the driveshaft and trans when reinstalling engine/trans is very difficult and dangerous
you should reinstall engine/trans, install flex donut/front driveshaft assembly on trans, then connect front driveshaft to rear.
Be careful as the engine comes forward the oil pan will have a tendency to hang up on the sway bar - keep an eye on this - you can lift the whole car very easily by pulling up when oil pan is caught on sway bar - this would be a very dangerous situation if it suddenly let go.
I find it helpful to use a small rolling floor jack under the transmission to guide the engine forward and to maintain a good removal angle.
Hmm - maybe a still better technique would be to just unbolt the idler from the frame - anyone tried this?
Yes, not for engine removal though - there is not enough give/flex in the tie rods to clear the bell housing - I did this once to check idler box motion (unless you turned both wheels outwards as far as they would go - still not sure you would have enough clearance) - remember the shorter (right) outer tierod is also connected to the idler.
Oh, BTW. To replace the rear crank seal at the flywheel, get a German "Goetze brand" stamped with the Audi and VW number: 056 103 051D in case you cannot find the original Alfa style.
Oh, and don't forget the ground strap!
There are a couple other things that are easy to forget - like clutch slave hose, fuel line(s), temp. sender wires. Good luck!