Series 1 tranny in Series 2
 

Yes I know Series 2 tranny are more robust and better gearing??? My ?? is my $6000 R3 goes in for new motor Friday under warranty, paying for just parts, 6 oil injectors, clutch, throw out bearing and pressure plate. I swapped tranny fluid but it is still not smooth shifting when at redline, no grinding just have to coerce a little. If the above doesn't fix it there are a few local S1 owners with rebuilt S1 trannys for free/on the cheap, to keep a fellow rotary owner on the road. I cannot afford a $2300 rebuilt S2 tranny at this point in my life. Can a S1 tranny work?

I'm not certain but I don't see why not. The S2 tranny will bolt up to an S1 so everything should line up.

You'll need to adapt the neutral and reverse switch wiring since the connectors are different between the S1 and S2. The shifter itself is different so you'll need an S1 shifter.

All of that said, have you tried flushing the clutch hydraulics, adjusting the clutch pedal, and checking the release bearing? All of those can affect shift quality.

My tech that replaced motor suggests clutch master and slave first.

Before flushing and bleeding? Seems odd.