Blinkers, high beams and front windows not working

Daughters car wouldn't start so her boyfriend tried jumping it. Long story short it ended up being the battery on the key fob now both blinkers, the high beam lights and the front two windows do nothing. We have checked all the fuses, had a new key made and had it put on a diagnostic obd code and it can up with a whole bunch of canned 2 codes which the gentlemen who charged us $85.00 for the test wants $85.00 an hour to find and fix it for however long it takes. Help please!