Are you able to check the progression holes just behind the throttle plate?

If these holes are blocked or partly blocked, then this would effect the transition from idle cct to main cct. But with the larger pilot [idle] jets currently installed, it may be disguising the blockage as the idle jet also would be feeding fuel to the pump cct. Also with the increase of the fuel delivery duration on the pump cct [as you mentioned you modified the accelerator arm] It may be now be over fuelling the mixture via the pump cct.

So many variables in these little animals...

Sounds like the pump nozzle is a fixed size [40] so I guess you will have to tune around it. Are you able to adjust the accelerator arm somewhere in between where it is now and where it was set before? [say 4mm travel]

Be sure to keep track of the changes and the effects you have trialled so far.

cheers
benny