Damn that sucks! I had some of the same problems and kept an eye on the shifter to make sure the routine was right. I actually had the thing whiff and not shift at all before. I was bagging a tenth instead of losing it and broke out. I highly recommend a Powerglide or a PPP shifter. Here is me eyeballing my shifter at Fallon in 2014. Bob Johnson photo.

I never knew consistency until I went to a Powerglide. The car is a tenth quicker with it as well! I have the same 727 with K's in great parts and it now resides in my street car. Super reliable but the thing would zerox 60' times then out of left field it would throw a 2-5 hundredths curve ball. The 3 spd. was inconsistent for Super Street as well and I was basically bagging a tenth and wheel racing for some wins. I never even calculated a throttle stop ratio until I changed to the Glide. So frustrating! Ironically I still use the SCS shifter for the glide. I had to replace the gate, drill and tap for a slap block and flip the solenoid bracket so that it bangs forward. ONCE! It works great. All C02 shifters require inspection and lubrication. It's just the nature of the beast when you are banging things with 120psi. If you are going to shift the SCS manually for the rest of the season don't GRAB the shifter when selecting 2nd. Slap it! Good luck with it!