The first thing I would do would be to run the codes to see if anything is stored. If not then I remove spark plug #1 and turn the crank with a socket until the motor is at TDC and check the timing marks on the cam sprockets. That's the most simple way, without removing the crank dampener pulley, to see if timing is off or not.
If it doesn't have any codes and the timing is dead on (even 1 tooth off can cause big problems) then move onto the wires. It would be a good idea to replace the wires since they are probably damaged. Wires are part of the normal 60k maintenance but it's not uncommon for people to get well over 120k out of the OEM wires, I had over 136k out of the ones on my old 91 and the car ran fine.
Make sure that all the vacuum lines on the back of the intake are connected properly. Make sure all the electrical connections are connected to their proper mates. perhaps when you had the intake off you missed reconnecting one.
I'm assuming that you replaced the tube seals and properly gapped the spark plugs, yes?
If everything has been done correctly and all the vacuum lines and electrical connectors are checked as being fine you might consider the cats as a problem. At night run the car until it's warm and then take a look under the car. If one or both of your cats is glowing red, that is a sure indicator that the red one(s) are clogged. The car probably would also be making somewhat of a hissing sound as well, kind of like a "WHSHHHHHHHHHH!" sound. Just listening for the whshh sound is not a 100% test however. A slight clog may not cause any outward symptoms other than a poor running car.
The above is only advice on where I would start to look for problems. I cannot promise that anything I've said is your problem. Best thing to do is start at the basics and don't replace parts needlessly, it can be an expensive venture if you do it that way. I once followed a topic here on the forum about a guy who replaced this part and that part, he spent well over $300 on parts by the time he was done and the car still ran like shiott. Ended up all that was wrong was a bad ground where he didn't tighten the ground all the way on the rear of his intake. Don't learn the expensive way. Take your time, us a good bright light when working in the engine bay and be thorough and meticulous when checking everything you touched while working on the car. The answer is probably right at your fingertips.
Good luck!
P.S. How did the car run prior to you working on it?