By bypass pipe do you mean where the three from each throttle body join the large one running to the map sensor? If so I suspect the changes do tot he vacuum leak could mess with it bad. since it is leaking the bike would think your throttle is open more load is on the engine at low rpm figuring the F to L switch point is in especially if it is in the lower throttle percentages where the map is assigned fueling from the map sensor signal. This could be why it runs better at higher rpms because you on the F table not the lambda tables.
@DEcosse is on to something there When I had one vacuum plug go bad I changed all and the lines to eliminate chasing the monkey again.