Tranny should be fine, the NV5600 is an unbelievablely strong tranny, I'll bet 6th gear synchro has bit the dust (grinds going into 6th no matter what you do) but that's a common problem, just learn to float it and be done.
As for clutches, all my dealings have been with South Bend Clutch, they are not cheap, but they are good units and I have had great service from them. With twins I would not look into anything less than the Con-OFE or FE, either one is going to run close to the $1000 mark by the time you resurface the flywheel etc. I would strongly suggest a Dual Disk unit if you plan to spedpull or dragrace very much, the single disk clutches just won't take the abuse. There are some drawbacks to the DD though, they rattle with the pedal mashed in, tend to be grabby until the 3rd or 4th time you do a 3rd gear burnout and they are costly, about $1400 or so IIRC.
Decide what you are likely to use the truck for the most, or how you are going to treat it ad make your choice from there. There are other good clutch manufacturers out there, all my experience has been with South Bend so that's who I talk about.
