Love the colour!
1Zs (up to 96) are common as muck and very cheap on ebay (£2-300 complete), but they are limited on tunability as the pistons are weak - 140hp max I'm told.
AHUs (96-98 ) are quite rare and more expensive but stronger and worth the money if you can find one. They can go to 200hp with the right turbo.
You can keep the immobiliser if you want to - its very simple electrically, and is a nice security feature. The transponder is very small and would probably fit a Polo key, or you could get a mk3 Golf key cut to suit your Polo locks.
If you want to get rid of the immo then the easiest way is to source an ECU from an early Audi 80 with the 1Z engine. They are electrically the same as the Golf 1Z and AHU, just with no immobiliser.
Are you changing the gearbox too? I think the 6N Polo diesel has a variant of the 085 gearbox from the mk2 and mk3 (86C), and I don't know how much torque this can take. You might be better off fitting the TDI box and driveshafts? You'd need the TDI shifter as the TDI is cable shift but that should be a simple bolt in.
(I'll have your old box if you do change it as I want one for a project!)
Oh, and I have the mk3 wiring diagrams when you need them.
My Corrado goes better with the standard 90hp TDI than it did with the 16V, so the Polo should fly! Especially when you start tuning it
Looking forward to seeing this :wink: