I was doing some engine maintenance on ProTek samurai and after taking the back plate I noticed some scratches from where the crank had been scratching the plate. Of course this was due to the flywheel sitting to far on the crank thus pushing the crank back and causing It to scrape the back plate. My question is how do prevent this from happening?

Keep the back plate off when you mount the flywheel keeping pressure against the crank while tightening down the nut. Usually works the best.

That's what I was thinking, but really strange as I never have seen or heard of anyone doing this.

you can simply pull the crank from the sg shaft side without taking off the backplate.
itīs a standard step while putting on the flywheel and clutch.

Won't tightening the flywheel nut naturally pull the crank shaft forward anyway?

no, because of the collet.
- pull the crank max out
- then put the collet on
- the the flywheel and the nut

You're right, I forgot the collet will clamp the crankshaft in whatever position it is in.

exactly

the rods will always rub the backplates so those marks will always be there..this is why Nova presses in a low friction ring into their backplates