Dheir

I know enough about vehicles to be able to change parts and diagnose simple issues. I'm not sure if I should know this or not, but here is my problem.
My battery died on me last night, right before it died the engine was running rough when I went to accelerate, probably cause I didn't have enough spark. So today I put a battery in from a vehicle that I just sold. I jumped it and it runs fine now. I did notice it running rough at first. But I think it took a minute for the battery to get a good charge on it. I pulled the tube off from the intake, it seemed to run a little better. I inspected some more, and the "Vacuum"? tube from the intake to the breather box, had a little bit of smoke coming out of it, it was black smoke. Is this normal? Thanks in advance.

EDIT: It's a 96 "XJ"? I'm not even sure what XJ means. with 262K miles on her. I just did a full tune up and replaced the fuel pump if that matters (doubt it).

99WhiteLightning

CJ CiviJeep or civilian jeep Round headlights CJ-2 "Agrijeep" flat fender, low hood CJ's with L-134 engine 1948 CJ-2A '45-'49 flat fender, low hood, "******" embossed on the hood sides and windshield frame CJ-3A '46-'53 flat fender, low hood with one-piece windshield design and a vent just below it CJ-3B flat front fender, high profile hood with F-134 engine CJ-5 the first V-8 in a short-wheelbase utility vehicle 1973; 1974; 1975; 1978; 1979; 1984 CJ-5A based on the M38A1 design CJ-6 20 extra inches of wheelbase than a CJ-5 1973; 1975 CJ-6A based on the M38A1 design CJ-7 extra wheelbase allowed for wider variety of drivetrain modifications 1976; 1979; 1983; 1984; 1985; 1986 CJ-8 '81-'86 "Scrambler" - 103-inch wheelbase pickup with lots of rear overhang 1981 VJ Jeepster Front end and drive-line from the *****'s Station Wagon; rear fenders from Jeep
trucks DJ Dispatch or delivery jeep Basic postal truck AMC 2WD FC Forward Control Trucks Dual rear wheels; heavy duty suspension and brakes; vertical cutout grille; round
headlights SJ Full Size Full-size Grand Wagoneers, full size Cherokees, full size trucks C-101 Jeepster/ Commando Part Jeep CJ and part Jeep Wagoneer MJ Comanche '84-'91 Compact pickup, Cherokee front clip XJ Cherokee/ Wagoneer '84-01 Uni-body construction YJ Wrangler '87-'95 Square headlights; lower and wider than the CJ 1990; 1991; 1995; 1996; ZJ Grand Cherokee '93-'98 Uni-Body construction 1994; 1997; 1998 TJ Wrangler '97- Round headlights, turn signals on front fenders 1997; 2000; 2002 WJ Grand Cherokee '99- More rounded than the ZJ KJ Liberty '02- Uniframe body; very upright profile