1995 Dodge Dakota runs and idles rough and feels like misfi

I just gave my 95 dodge dakota 3.9 a tune up and it was running great for awhile, now it seems to be idleing and running rough, and feels like it misfires when I speed up unless I gun it. It almost feels like its running out of gas, but I know there was at least 2 gallons in it because when it started acting up the low fuel light came on (gauge dont work) after I put about another 3 gallons in it the truck started running better, could there be a problem with the fuel delivery system, or maybe a bad filter? And sometimes when it acts like that it feels like it has no power on the highway.
Note: the truck sat outside for about 2 years before I got it, ive put about 400 miles on it sense I got it.
could it be I need to keep the tank full for it to run good?