Carb (OEM) - Main Jet: 97 M900

[greenohawk69]

I wound up putting both main jets in upside down (see attached picture) in the carb.

Is that going to be a problem?

Actually had one upside down when I removed the old jets, emulsion tubes, and needle springs. Installed a new Factory Pro kit.

[motorcycles]

Yes, I imagine this will have an impact on the way the fuel flows and vaporizes.  Correct me if I'm wrong here, but I believe the stubby end with the o-ring goes in leaving the narrower end protruding.  The bike may start up and run, but I'd want to go back and get them properly oriented if I were you

[greenohawk69]

Yes, the stubby end with the O ring goes in first.