Engine light and driveability issues after engine install

[Wilson01S]

Well took a little longer than expected at the body shop! HA! I decided to have the whole gone refinished.

Anyway. Car is back and I still have the issue. Sputtering/hesitation off idle. Seems to drive ok at cruising speed, but I do get a occasional misfire around 55mph. I am going to replace the MAF since all fingers are pointing to that as the obvious.

Also I have a new issue where when the car is shut off and key removed the fan behind the passenger side air inlet runs for ~90seconds before shutting off. Also when idling it turns on and off very quickly. If I remember on my dads 98 box it will run as a normal cooling fan for a minute or so and then shut off. This fan seems to come on and off at a much quicker interval.

Any ideas?