Chris,
I have on a couple of occasions, had the same "run away" syndrome with "proven" LA46's. On one more memorable occasion, the run away went on for several weeks while I tried everything I could think of. I even took the head off and scraped the piston top. It was about that time, although I would not want to say it was necessarily related to that scraping of the piston, that the problem simply went away. I liked Balsa Butcher's comment about the synthetic to clean the engine. I will certainly add that "fix" to any problems I encounter in the future.
I log my engine hours and my oldest LA has an estimated 280 flights. (I estimate engine run hours by multiplying each flight by an arbitrary 6.5 minutes.)
As for the Xoar props, I have almost exclusively moved to Xoar for the reasons you note. In my humble opinion, they load the engine as I like and I almost always get good engine runs. I have a scratch "Green Box" Nobler that comes in at 53 oz and I run an LA46 with a Xoar 12 x 4. I have tried the APC 12.25 x 3.75 on other planes with LA 46's but they just seemed soft in a lot of the overhead maneuvers. I have converted all of my LA46's to either ST51 or Randy Smith NVA's. In so doing I found I had to drill out the venturi to about .287" to get the power to adequately turn the 12 x 4. That did cause an increase in fuel consumption so I added an extra head shim and am still testing that set up. I did improve the fuel use over the single head shim but am still testing for any power changes. (A 7.3mm drill bit gets the .287" size.)