The instrument cluster speedo signal shutting down is a sign that your system voltage is dropping below a sustainable point as it had no charging capability and your bike was running off solely the battery, which would be discharging progressively being in total loss mode.
You validated this by finding fuse 2 blown.
You will need to re-charge your battery from a charger & it should be recoverable.
As to the primary problem, it sounds like it may have been related to the modification.
At this point I would suggest that your bypass the OEM fuse-panel completely and run new wires from the output of the Rectifier/Regulator assembly directly to the battery. This is similar to that shown in the thread referenced above, while still retaining your OEM Rectifier/Regulator.
You can also follow the directions in
this thread