DIY 2 DOF on a budget

The DIR box being checked orange in Axis Assignments or not determines which way each axis moves, this is what SimTools expects: https://www.xsimulator.net/community/faq/which-way-to-set-simtool-axis-movements.230/

If pitch responds in Output Testing, which is where you should check Axis Assignments before messing with games, then roll should as well, if correctly configured. Is Output Testing working as expected?

As an aside, looking at your existing Axis Assignments, be mindful that the the total allocation should be around 100%, or just a little over, in total: https://www.xsimulator.net/community/faq/axis-assignment-percentage-totals.120/

SMC3 is where the motor control and related response characteristics should be tweaked.

If SMC3 is working as expected and nothing changed on the SimTools side my best guess would be the likes of antivirus interfering and disrupting communications.

Try temporarily disabling AV and test, sometimes AV interference also forces a SimTools reinstall if it has messed with SimTools files.

It would depend if the jerkiness is the result of settings or hardware, or both.

Can you please post pictures of all of your settings.

There seems to be a bit of noise associated with SMC3.

With respect to SimTools settings for flight sims you can get away with much higher axis allocations, particularly for roll and pitch, which should be the dominant axis that are set up and refined first, before fiddling with any other axis. Surge should definitely not be the dominant axis.

In conjunction with that, the larger the Tuning Center values, the smoother the motion over a larger range.

So start with roll and pitch, set the axis allocation to say 80% each, capture the Tuning Center values, which will likely be higher than what you currently have, and tweak from there. As long as the jerkiness is not hardware related that should help smooth things out a bit.

If using roll and pitch, rather than rate values Extra 1 and 2, use the Anti-Rollover checkbox. Anti RollOver is designed to eliminate the 180 degree in-game inversion in rolls and loops.

80% for Axis 1 and 2 for both roll and pitch, in GA you are unlikely to be at max range concurrently, aerobatics or flight combat would need to be a bit more conservative.

Also initially set the Tuning Center to 80 for both roll and pitch, but then immediately do a capture in the Tuning Center after flying around a bit, pushing the edges of the flight envelope but not crashing.

It really depends on the design of the rig, 75rpm would likely suit most designs, but others could work depending on how much inherent design leverage here is, as there is a tradeoff of torque for speed.

The closer the motors are placed to the pivot the greater the torque required to drive the rig, conversely, the larger the design leverage in placing motors further from the pivot the less torque is required.

SimCalc is a good way to explore the tradeoffs in design Vs physics: https://xsimulator.net/community/faq/simcalc-calculate-linear-speed-and-forces-of-your-design.270/