We ran UNI pod filters. Like others said this really made the jetting easy.
As for the counter balance shaft. You can't take it out. It drives the oil pump I believe. But we did install a straight shaft to ditch the weight. No issues, worked fine.
We also ran different needles, I would have to do some serious digging to see what they were. I believe they were the ZR needles.
We also ran the 4 degree timing key, PSI pipes and stingers. I know, I know PSI. But man they worked well.
We always spun them up around 9100rpm. Ran a yellow secondary spring with a 49deg helix. And 18/40 gearing. Could have been 17/39 gearing. Again long time ago.
Our biggest problem with these motors was the counter balance gear for the oil pump. It would bust a tooth then would bind up knocking the bottom end out of the thing. Was a very sick feeling to be in a good climb then BAMM!!
Here is an old video that I posted in the Video section years ago.
Man those triples sound good. I miss that.
Thunder
http://www.snowest.com/gallery/video/28.wmv