If it is what i think it is, i had a very similar problem on exactly the same set-up on an off-road race car. Haltech uses a thing called a reluctor adapter which converts the signal from the crank angle sensor into a form the E6A can read. This proved to be the weak link and caused all sorts of tuning problems.
A fix used on mine was to use the guts out of a Pulsar distributer and throw away the reluctor adaptor. I have this set-up on a silver top 20 valve running the same ECU and it runs faultlessly.
For tuning, I used a guy running out of a factory next to the Australian VW Performance Centre in Croydon (vic). He has good experience in running Haltech computers and was the one who sorted out the problems with mine.