First, the check engine light is indicating a problem within the electrical / ignition system. That could be causing most, if not all, of the engine problems you are having. You need to have the computer scanned to identify where the problem is coming from. Most parts stores will do it for free.
As far as the clunk you get when shifting gears, that could be a few things. Check universal joints, free play in the differential, and make sure trans and motor mounts are in good condition.
As far as the ABS light, it is most likely a bad sensor. Have it scanned too.
Now for the noise. Make sure the coolant and all other fluids are full.