Be sure to check your IAC on your throttle body. I think its called the Idle Air Control. I had some of those symptoms and did a tune up, replaced the fuel pump and some other things and it ended up taht i just needed to clean the IAC. 5 min and i was done and it ran smooth.
It works 60 percent of the time....every time.
I currently own 2000 Wrangler TJ 2.5l, 1988 Grand Wagoneer 5.9l. I have had 1993 Cherokee 2.5l, 1997 Cherokee4.0l, 1986 Comanchee 2.5, 1985 grand wagoneer 5.9l, 1993 Wrangler 2.5l, 1998 grand cherokee limited 5.9l, 1986 cherokee 2.8l, a 1990 Wrangler 4.2l,
1990 Cherokee 4.0l