Ditch the 0.035
This sounds crazy but is true.. Your PowerWave will pulse better even with thin pipe lands if you use 0.045 filler... This is especially true with stainless. Your Lincoln rep should have advised you of this from the very start.
Use the programs already installed in the powerwave. I would be shocked if the pre-designed programs were not just the right thing. Wire feed and trim are the only adjustments you ought to need once you have the right program set on your wirefeeder.
Self/Custom programming a machine as complicated as Powerwave would take some very special training.. There are way more than the 6 common variables used for pulse pendants of the past.
To tune in your machine inexpensively for pipe roots use 3/16 sheet coupons tacked with a 3/32 gap and 0.045 wire. The STT function should get these root passes full pen with a single pass, maybe a light cover pass if there is slight concavity at the face. Roots will be perfect by the third try.
For cover and cap passes on your pipe welds, STT is turned off and the synergic pulse program for that particular alloy (steel/Stainless/Alum) is selected, the inside coverplate on your 10M feeder will give you a synergic pulse selection for your 316. Arc length is controlled by the "trim" knob and travel speed is dictated by Wire Feed settings. Cover and cap passes may also be accomplished with traditional spray transfer in the flat rolled posintion.
For pipe welding the big money is being spent for the STT roots and the ability to get spray transfer out of position with the synergic pulse. If you dont need these things don't spend the big money..... Now your training environment is different.. You want to be able to train for multiple processes and situations. (at least thats what I tell my boss when I ask for $8,000 power supplies) :)
One last tip.... The wire feed settings for 0.045 synergic pulsing in the Vertical and Overhead positions may be very low compared to Traditional Spray settings you are used do, Don't be afraid to turn your WFS down to 150 or lower in trials to discover how to get puddle control going vertical with upward progression. With that 0.045 wire and miminum WFS you can pulse weld 0.063 stainless sheet fillets with no burn through in any position with spray transfer quality.... it really is stunning.
If you try these things I predict you will be a very happy guy.