To fix the axle binding problem all you have to do is get 16v mk2 axels they are 3/4" shorter then the mk3 axles. As for the control arms I don't think there is any difference from mk3 to mk2 just the subframe is different.
I found a 91 jetta gl on craigslist with a 99 aba swap. It is the entire engine,trans, dash and cluster swap. As the owner explained it to me, the driver side axle is binding because the mk3 control arms and driver side axle are too long. I'm being told that to get this thing back on the road I need to get a mk2 driver side axle and mk2 lower control arms. I've been searching and can't find anything on this subject. I found one thread that seemed to hint that the entire mk3 subframe can be swapped without issue but it made no mention of control arms or axles. I've tried the mk2 forum but hopefully I can get some faster answers here.
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The control arms are different, I almost F'd that up years back.