well, I have the 4.0, but I imagine its the same. I assume you have everything off, and you are beginning to put it back on. you put the exhaust on first, and put the 2 outer bolts on loosely to hold it in place. Next, you put on the intake manifold. you can line it up accordingly to the hole, and the bolt should go between the intake/exhaust manifolds. put the bolds on in a clockwise and outward path...starting in the middle working out. couple words of advice...1. always put on a new manifld gasket. 2...make sure you toque all the bolts to the proper torque, and recheck them about a week or so later, mine were 13 ft.-lbs I believe. hope this helps, if you need more info let me know.
'93 YJ 4.0 3" RC lift 15x10 wheels and 32" tires.