you need to fix that exhaust leak. drill the old broken stud out and put new bolts and nuts on there. a leak there can cause it run poorly.
you really should have headers, or at least a 3 inch down pipe and a plog.
if you have a droid phone get the toque app, and the obd2 blue tooth scanner, app is 5 bucks, the blue tooth obd2 is like 10 bucks off ebay. it will scan more live data then you can shake a stick at.