Flashing hold and Check Engine Light...

I have read all over this forum that this is a pretty common problem. The Hold Light and Check Engine Light all the sudden started flashing on Thursday.
Was losing power and rough on take off Had it scanned and it came up with the Throttle Position Sensor and CYL #3 Misfire. Replace the TPS and the coil...
Drove it after the parts were installed and its fine up to about 55 Mph.. then it starts jumping like a misfire. The hold light and Check engine light are flashing again... any ideas?? This car has had a new timing belt and transmission... however sat for over a year before I got it and start driving it. It has been great till now...

ETA: Got some codes this morning...
P1121, P0101, P0122, and P1624.. Husband is thinking it may be the MAF sensor... also it has Ford Sparkplugs, will be replacing with Factory recommended spark plugs at the same time

1624 says "a code has been sent..."
The rest is relevant with MAF and TPS....but begin with cleaning the sensor contacts, sockets; long time with moisture helps bring those problems. I would not go as fas as suggesting soldering the wires directly to the sensors, as some suggest, but do clean and test.