Diesel Bombers - 06 f250 starting issue

Hello. This is my first ever post to a forum so please forgive with me if I'm posting wrong. Have always used forums for the info and advice that has already posted for other people but this time I ned to ask specifics. So my truck is a 2006 f250 lariat four wheel drive. It has a 6" lift on 35x12.50x20s as far as performance just your basics, sct x4 with canned tune, Mbrp 4" turbo back and K and N cold air kit. So I'm pretty stumped and also at work so not able to work on it at the moment but last Thursday As I was pulling into a parking lot I had the low oil pressure display come on and gauge drop to zero. So I pulled over and was trying to figure out what was going on and as I blipted the throttle it went back to normal. So went home and started doing my research. It did it a few more times at idle but kept clearing up. So all the reading and after checking my oil level and truck never ran bad never died or sputtered I decided it must be the switch. The oil change was past due so I went and got motocraft oil filter, fuel filters, and rotella 15w40 and a new oil pressure switch. I got called out for work so last night I changed the oil and upper fuel filter. I haven't done the bottom yet because I didn't have a 36mm socket but I did go ahead and drain the water separator. Anyways filled it up with oil cycled the key a few times and it fired right up oil pressure came up and I turned it off. So with all that said for a long time when cranking it it has sounded like it was a little sluggish but always started. I changed the alternator out about 6 months ago and other than that never had any problems. So this morning I went to start it to go to work and it sounded real weak. It did start but after about 3 seconds started running real bad and died. I hooked my tuner up and turned it over and as I figured only 6 volts while cranking. So I took batteries to oreiley had them tested and one was bad. Got 2 new batteries installed them and it cranked over better than ever but just wouldn't start. Finally after about 30 seconds it starts ran like shit and after I finaly got it to idle it idled great and sounded good. As soon as you throttle it it would be rough. To me sounds like it was maybe having fuel delivery problem... So I hooked my tuner again to it to check what was going on and I was only showing 12.5-12.8 volts like the alternator wasn't charging. I will have it tested tonig but anybody ever have any weird stuff like that happen or have any knowledge they could share I would really appreciate it. The whole time this morning I was praying that my ficm wasn't toast.. I know low voltage can cause it but I figured ahh just had a bad battery it happens. So anyways I'm stumped. I apologize for the long post I hope it all makes sense when reading