Gear shift and check enine light

[mouseakins]

98 Pontiac Sunfire
2.4L engine
automatic

My roomate just finished replacing all the fluids in my car and recharged my battery after it wouldn't start, wouldn't shift, and the breaks wouldn't work. Once we jumped it the AB and break light wouldn't turn off. Now everything is cleaned and works but when it shifts into go it jerks really bad and I hear a faint rattle or scratching noise while driving. The ETS and Check Engine light also remain on. He said he put in 4 quarts of transmission fluid (as the book says to do) but thought that might be thr problem. Any ideas on why the engine light, ETS light, or the jerking/noise is occuring?