My SP13
Just completed my SP13 a few days ago.

One minor hiccup was that the heads of the #6 screws on the ratchet were running into the spokes of the ratchet wheel. I solved the problem by boring the countersunk holes on the clicks a bit deeper, just by manually applying an 8mm drill bit. Otherwise it went together without issues. Nice design!
I did very little additional prep before hanging it up and testing. It ran OK for a few days with a 4lb 6oz temporary weight (no pulley). Then it stopped and refused to restart. So, now on to the tuning.
The bearings I had on hand all had metal seals. I soaked them in a little cup of "Goo Gone" to try de-greasing, which seemed to mostly work... but I'm getting new bearings tomorrow with rubber seals, so I can do it by the book. Got some graphite lube coming too. Will report my progress.

That is the first time hearing anything about the click screws rubbing. Flat head screws should sit nearly flush and have enough clearance. You have a solution that also works.
The pendulum support bearings are easy to check by running the free swing test. Anything greater than 10 minutes should be OK.
The escapement characteristics after the clock stops can tell you a lot about what to debug next. Does the escapement still spin? If not, then look for defects on the gear teeth where they are meshing. Also check for end shake on all the arbors. If the escapement is sluggish, then look for friction. Make sure every gear spins freely on its arbor.
You need to hold the clock level when running without the pulley. It is a simple way to double the effective weight, but the balance is off so the frame wants to tilt and the clock will be out of beat unless the clock is held vertical.
Your clock should be very close to running perfectly.