It is rare but there could be some bad machining when they bore the holes for the dowels, the clutch could potentially not be aligned properly (the plastic tools suck for a twin disc... use an old steel input shaft (unuseable) to make installing a twin disc much easier..... or I've seen it on my own Chevelle build that the input shaft came in contact with the recess in the crank.... I actually had to cut off a 1/4" off the tip of the input shaft (after trying everything, calling Quicktime etc) to make it slide together. THis seems to only be on truck crankshafts not typically used with manual transmissions I guess (my alum 5.3 is from a Trailblazer)
Sometimes the T56 Magnums need some of the casting ground back on the front cover where the slave cylinder pokes out the side of the BH..... as they can bind up when trying to tighten them down. Seen it in probably 50% of them.
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Project: 1969 Chevelle, alum 5.3, GTS76 turbo, Chiseled Perf A/W intercooler, Holley Dominator EFI, Davis TC, JRi coilovers, 14" brakes, T56 Magnum. CTS-V Recaro seats!
Coffey Fabrication Nashville, TN doing the fabwork! 800rwhp+/25mpg+/9's@150mph goal 
https://lateral-g.net/forums/showthread.php4?t=52976
1993 Mazda FD RX-7, built LS7, T56 Magnum, Holley HP, Davis Tech TC, 8.8" 3.73 Cobra IRS diff, DSS axles, Ohlins coilovers, big brakes.
CCW 18x11 front 315/30/18's and 18x12.5 rear on 335/30/18 RA1's, 2850lbs
10.31@137mph 165mph Shift-Sector 1/2 mile speed
441ci AllPro headed motor and 200lb weigh reduction in the works....
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