Long story so bare w me. About three weeks ago the egr cooler on my 06 F350 6.0 ruptured.I welded the cooler and while I was in there I changed the oil cooler too.Got it back together and have been driving for the last couple of weeks.Went about two days before the check engine light came on.I knew it probably would since its an 06 and the egr cooler is welded.I have turned it off a couple of times w my phone,went to turn it off again today and it also had a P0261 code (inj circuit low cyl 1). Pulled the alternator back off to check the #1 inj connection,wires looked good and the pins weren't noticeably bent.reconnected it with a snap and started it back up.After few minutes of running(at speed) I checked it again and it said "pending fault code" but no check engine light.After some driving the light came back on. Checked the FICM voltage and it was 48.5 and the alt voltage was 13.5.Battery voltage was 12.8 w the engine off and drops to about 11.8 when cranking and builds back to about 12.4/5.Batteries are 6 years old.I have also noticed some extended starting times for the past couple of months and I had to jump it to restart after the cooler work.The truck sat for about two weeks w/o being started.I plan to replace them both Monday when the Ford place opens. Truck has a small skip at idle but is not noticeable by the gauges or seat of the pants at highway speeds.Light seems to come on after cranking and I can turn it off and it will stay off until I turn the engine off and restart. With the exception of the welded cooler the truck is all stock,no tuner,has the factory air filter and even the converter on it.Any thought's or things I could have missed??