[T77911S]

ROW or USA
not sure about stage 2 or 3.
none of this should effect the alternator. you may have moved something that did not have a good connection that is related to the alt.

wow, where to start.

for the pump that runs all the time:
check the connector on the top rear of the air flow meter (AFM).
if it is not connected that is why the one pump runs all the time.
if it is connected, remove it and see if the other pump will also run all the time.
leave it off for now.

if one pump runs then the other should too.
check the relay and then check the socket for the one that does not run.
one of the contacts on the socket may need to be closed up some.

just to compare the 2 relay sockets, check for power on both sockets from pin 85 to 86.
if no power then check from pin 86 to chassis ground
with key ON and the connector on the rear of the AFM removed.
if you had power from pin 85 to 86 on both sockets, plug the connector back in on the rear of the AFM and repeat 85-86 test. you should NOT have power

if the rear pump is still running all the time remove the yellow relay in the engine bay on the relay panel. (don't know for sure if the 89 is yellow). check to see if it still runs