you need:
complete linkages including gearstick from 1.6-1.8 manual
driveshafts from 1.8 carb/gti/16v
fuel pumps & matching lines from 8v/16v GTI
engine brackets from 1.6-1.8, gearbox bracket on 2.0 will prob work?
exhaust system will be tricky, is anything included on the 2.0 lump? you need a lambda probe for it ideally. the 2.0 manifold is the same as the 1.8 MK2 GTI manifold, soi if fitted you can use that. If you have the 2.0 downpipe you can use that, just need a pipe to go between it and your chosen exhaust system, decent zaust place should be able to make you one up. Not sure what bore of the 2.0 system is, it may be the same as a 16v system so a mk3 cat bypass pipe may work. Other option is G60 downpipe & cat bypass, fits straight on a MK2 16v zaust system.
fusebox is all well & good if the 1.3 is a 90spec, if not you'll also need to convert the 1.3 to 90spec wiring, or splice the mk3 loom to the 1.,3 fusebox. other option is to have the head off and fit a MK2 digifant one, plus managment. If you do go with MK3 managment, keep the MK2 1.3 coil, TCI & loom, bin the crappy mk3 coil. To make it work you need to keep the 2 fusebox wires to the coil, and splice pin 6 from the TCI to the ECU trighger wire on the MK3 coil plug (red/green)
Ideally while engine out fit a front arb, GTI rear beam with arb and some decent brakes!