You've made things worse by replacing more than what was recommended. The MJE350 and PN2907 on the center low current board were working properly and giving the correct voltages, now they are not.
This is about the point where sending the kit in for repair starts to make a lot more sense than continuing here.
Very interesting development. I didn't see this message until now. So I also replaced the LM431 on the B side on the low power board but not the other two. Now Voltages look better and when listening with the tubes in it sounds much better. No buzzing but the overall volume seems lower. There isnt and significant balance issue on each side
But there are still some discrepancies.
With the 6AQ5s on the Low current board the OA and OB are low as well the IA and OB on the high current C4Ss are out of range.
With 6AQ5s
Low Current C4S
IA 149
OA 45.6
KregA 5.93
bRegA 148.9
IB 149.5
OB 46
KRegB 5.9
bRegB 149.5
High Current C4S (closest to power inlet)
IA 199
OA 149.5
bA 0
IB 0
OB 79.7
bB 149.5
High Current (furthest from power inlet)
IA 199
OA 148.9
bA 0
IB 0
OB 75.8
bB 148.9