Due to the time difference between myself in the U.K. and Tekno in the U.S.A I communicate via e mail and I've had nothing but fast and polite help from Daniel at Tekno.
I have the same issue with you in so much a my screws stand proud of the chassis and Daniel has advised me to swap them out to M4 x 12 & M4 x 16 screws as some of the chassis were mistakenly countersunk for M4 screws. It's slightly annoying but for the sake of the price of a few screws I'll do it as otherwise the kit is spot on. I never had the problems with the spacing on the clutch that you've had so I don't know what went on with yours. I'm running a 1515-1Y so I don't know if the shaft is slightly different?
Anyway glad to hear that your sorted as personally I've found Tekno to be really helpful.