1.9 should pretty much be the same... it's the passenger mount that's the biggie.
the engine swap itself I am not to worried about. its the getting the 1.9 to fit correctly and have mounts line up i am in turmoil about.
I think i will be using my old trans
Just buy a Prius and be done with it...
Just buy a Prius and be done with it... 
I Think Jeremy MIGHT want the ability to stop
Some 1.9 pumps mount the exact same as the 1.6 pumps. It's the 2 piece ones that are different. If you get a single piece pulley just use the mk1 motor mounts, swap the mk1 coolant flanges and bolt your tranny up to it and away you go. Exhaust will be different as well.
If you do get the 2 piece pump style then you need to modify the mounting bracket. It's a matter of using a mk1 gasser motor mount and cutting the stock mk1 diesel one.
After really taking a look at most vehicles driving around.. it appears they are all TDI Mk4's...
Should I bite the bullet and start to put together a TDI swap piece by piece?
As first swaps go I'd personally not recommend a TDI... it's an orders-of-magnitude increase in complexity due to all the electronics: under the hood (ECU etc), the cluster, the immobilizer ignition system (post 2000), and the mechanical stuff: the speedo, the clutch, shifter, the pedal cluster...etc etc etc.
Plus if you get a mk4 TDI you will need custom motor mounts. If you get one from a mk3 then it is bolt in.