There are basically 3 types of ECU for the pre Bugeye turbo's.
4 plug (96 and earlier, V1-V2)
3 plug (97-98, V3-V4)
3 plug (99-2000, V5-V6)
The enormous amount of different ECU types using the same physical connectors is just because of specific mappings available for different countries/gasoline quality etc, but as you'll be working with a mappable ECU those are not of concern to you as you'll only need to find the ECU which connectors physically fit your loom.
The first one is pretty obvious, if the ecu has 4 plugs it's a 96 or earlier.
The difference between the 2 3 plug types is that the later models (99-2000)
have much more pins per connector..
The V3-V4 have 3 plugs, containing 16,22 and 26 pins respectively, all in 2 row pinouts
so you'll end up with thin narrow connectors
The V5-6 also uses 3 plugs, but they each contain 32 pins, and they are much higher
and narrower physically , and arranged in a 4x9 pin format.
There are pictures of the connectors in the link below.
http://www.jollygreenmonster.com/pinouts.htm
Do you plan on selftuning or going to a shop??
It usually is best to go with the ECU the tuner has experience with IMHO, so I would consult him as well.
Also ,seeing that there are more then enough PnP ECU's available I would not bother with the Haltech (again IMHO)