Strange that the fuel pump cuts out, does the fan try to start as the fuel pump cuts out? maybe a short or lack of volts stopping the fuel pump as the fan cuts in.
Did you have this issue prior to fitting new parts on the bike?
Overheating is mentioned on this thread but no follow up was written:
New Transalp 700, overheating?
I would in this order: check coolant mix first - you could try some engine ice and I would flush the radiator out. Then look for fan issues - including a short or a seized fan, blocked or damaged fins, then look at the thermostat or temperature sensor, you need to figure out why the fuel pump is cutting out, so check volts across the battery as the engine overheats and the fan tries to cut in and see what is happening.
Good Luck!
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