Just a few thoughts from me... apols if they are all too obvious or already considered and ruled in or ruled out...
1/ I cant see how doing the very straightforward Riko mod would be likely to cause any of the problems described... particularly if the mod was done by simply removing the six screws under the track piece and then reversing the two powerwires to one of the lanes. This does not require any access to the internal electronicswithin the powerbase... so no damage to the powerbase would be likely. I would envisage the worst kindof problem might be dislodging connectors to the sensor boards. I do however recognise that doing this mod is likely to invalidate the manufacturers warranty. In summary I dont see the carrying out ofthis mod as a likely cause of the problems experienced.
2/ I have found the use of the pace car feature can cause instabilities in the app from time to time... for example both a pace car and anon pace car registering laps under the same driver in the app. So if there are other issues you are seeking to addres I would recommend a fresh install of the app and then to avoid selecting the pace car function until you are confident that everything else is functioning correctly.
3/ with the clean app install I would then systematically look to see if cars perform identically both with and without the app running. i would ensure that profile C is used for all cars and thatthrottle is set to 100%. Remember, this driver nformation is only uploaded to the powerbase when you hit prepare to race... until that point old values remain in play.
4/ I would look out for a rogue car with perhaps a failng motor, or intermittent pick-up, or poorly fitted decoder... as factors which might be creating a sense of overall inconsistency of the system.
Hope a solution comes into sight soon... this system is usually pure fun... so hopeyou get into that mode very soon... good luck!