Just wondering if you spun the cam drive chain or if it's just wore out.

Don't know if this has been posted, but have you checked the voltage on your TPS , and have you adjusted your IAC ?

Now that you've got your timing set and you know the MAF is good start with the basics. Clean the throttle body really well. Those get really dirty on the tpi and make it run like crap. While youre in there take out the IAC valve and clean that too. Also check all of your vacuum lines and set the tps to the proper voltage. These are common issues with the tpi that often times make it seem like you've got a more serious problem.