Not good to hear mate. I had a similar issue with my ae101 conversion into my ae82 years ago, but I'm farked if i remember what the problem was, and how i fixed it. I have a feeling the "throw" on the shifters were a different length, or had to make a combination of the 2, and had to make the ae101 shifter fit. Shit I can't remember. Sorry i can't be more help Luke, hope you get it sorted soon.
Also remember having to ʞ©$ɟ around with the shifter cables for some reason, it was 5 or 6 years ago now.