I'm pretty sure the same synchros and hub selectors are used regardless of which gears and R&P you get. So if you are getting grinding when shifting to third gear at high RPM with the stock gears, and it's due to worn hub selectors and synchros, then you will still get the same grinding with short gears and short R&P... unless you replace the hub selectors and synchros when you replace the gears. (Which any good mechanic will know enough to do when he opens up the transmission and takes a look at them.)
I changed out the whole set of short gears r/p, the machanic replaced my second synchros cause the it worn out, but I never have any grinds when I have my stock gears with r/p.
Most dealerships will warranty the installation of any parts purchased through them, but will probably not warranty the installation of any parts purchased elsewhere.