I changed my clutch last year and had trouble with the throw out bearing. The old clutch was the three finger type and the new had the vanes. I put in the new clutch and had the same problem as you are having, I took it out and put in the old throwout bearing and it worked fine. You may be able to adjust the throw out lever ball stud in the bell housing, I've heard some are adjustable.

The parts store guy is probably just reading what it says in his catalogue from the manufacturer and they seem to be wrong as much as right. The flywheel they had listed for my 428 had a register for a small flange crank and mine is a large flange and the clutch disc was an 11 inch and would not fit inside the bolt hole pattern for the 10.4 inch clutch, yet all were listed for the 428 and the 428 equipped cars in the parts book. After going by boat to SS island three times to return parts I tried the napa in Sidney and they got me a clutch after I took the center-force number into them. They couldn't seem to find me a flywheel although the store down the road could get me four different brands. I had the flywheel resurfaced, through away the throwout bearing and the chevy pilot bushings that cam with the clutch, and everything works well now. It cost more when you have to replace new parts, but at least I have a 428 not a 396 or 427.

Info I've read but cannot confirm:
Pilot bearing #7109- GM part #15533265 slip fit with the cover facing out stake to retain;
Pilot bearing #6202 may be used but pilot bearing hole might not be deep enough.

The pilot bearing I got with my Tremec tranny kit was a National #7109