2001 Ford F-150 2001 F-150 running rough. Help!

Hi, I started my truck yesterday and it idled good, but when put in gear felt as though it was missing and also while driving, especially in OD. The SES light started flashing and then stayed on. I checked the code with my Hypertech PPIII and it was P0125, Insufficient Coolant Temperature to enter Closed Loop, so I replaced the thermostat, the temp sensor, and since it had 199000 on the original plugs I replaced them too while I was at it. It still "misses" badly so I suspected the COP's and went through and unplugged them one at a time while the engine was running and believe they are all throwing spark, by the way each missfire code showed up as they should for each cylinder when I did that. Now the code P1000, OBD-II Monitor Testing Incomplete, came up and I cleared that. I am now suspecting an injector may be partially clogged? I'm thinking that because while driving it today it seemed to work itself out of the problem once in a while and run great, but then would continue to "miss". I'm also thinking I should replace the O2 sensor. A local mechanic suggested my MAF sensor may be bad so I cleaned it with no effect. What is your take on the issue? What would be the best way to clean the injectors? Is it possible that one of the coils could be weak? This is the first time this pickup has ever had any problems so I cant complain too much about it! Thanks for any thoughts.

Big boys love big toys!