Define crap. All the time? Just when you get on the throttle? When you squeeze the throttle soft or hard? Be more descriptive on what crap is. There are a lot of parts to a motor and vague doesn't help narrow it down.
Screws will make the ski run less than perfect but not "like crap". It can run "okay but not great" with everything working right and bad screw settings.
Here are the jetting specs for a B-pipe on a stock motor...
http://factorypipe.com/media/instructions/yamaha/701SJ03.pdf
Main Jet: 135 (130 stock)
Pilot Jet: 70 (stock)
High speed screw: 1 2 turns out from closed
Low speed screw: 1 1/4 turns out form closed
Needle & Seat: stock (55 psi)
Spring: Stock (95 gram)
Set the carbs to the specs provided by FPP. It may have a slight hesitation but it will run good overall. If not, you probably have another issue. Clean and test your carbs. Put in new plugs. Ensure the fuel system is clean, etc. Then worry about jetting when it works kind of right.
PS. Stock pop-off is 53 with 1.5 N&S with 115gr spring. Not sure why FPP says 95 gr spring.