Take a look at the new plugs that you installed, they will tell you what it's doing.
Black, its running to rich, white/gray is too lean, light brown is the color that you are after.
And stock champions or autolite are the plugs to run. Don't waste your money on those big fancy expensive plugs, since you don't have a big fancy expensive motor for them to go into.
Sounds like you might need to clean the throttle body, sometimes they get carboned up to the point where sea foam won't even clean it out. Check and clean all of the electrical connections to the throttle body as well. Those mean a lot with that TBI injection system.
'87 YJ, 4.2L built and bored, 8" of lift, 8.8 rear, AX15/NP 231J, Tom Woods drive shafts, Flat fenders, 12,000LB winch, Custom bumpers, Rattle can paint job. Never completed...