The black thing your throttle cables go into is indeed your throttle housing, the TPS is on the side of the carbs (if the 6 has one, which I don't know), and measures how open your throttle is to adjust the bike accordingly.
Personally, I've never filed the locating pins down, as they're there for a reason. Drill the bars instead, and you'll have the job done properly, with no risk of the controls moving at all.
Get the bars, pop them in the clamps and do them up loosely. Sit on the bike in the normal riding position and get the bars positioned to where they feel most comfortable, then do up the clamps. If you feel the bars are too wide, get your hands into what feels like a comfortable position, mark the bars and hacksaw the ends off (i've always done this on renthals as they're quite wide stock, and I don't like that at all). Once you've done that, measure how far in the locating hole is on the stock bars, and at the rough angle, mark it out on the renthals, check your measurements, and drill the right size hole.
Voila, job done
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