Rough engine

Playing with the distributor is not a good idea, the ignition timing setting is very critical, I would have a tech re check that the valve timing is set correct and re set the ignition timing correctly, also a diagionsis scan may shed some light onto the problem, start here.

Mark (mhpautos)

There are a few things that could be going on that will need sorting through as it sounds like a combination of issues are at hand.
First, I would be concerned about the timing belt being off.
Is it one camthat is off? Is it the intake or exhaust cam?
Did the shop that repaired it do the timing belt?
There is a possibility that a valve could be bent if the timing is off enough. Do you haves the means to do a compression test?
If not get a infra-red point and shoot type thermometer. With the engine at running temperature, measure the temperatures of each cylinder. If there is a cylinder that runs colder than the others, by at least 50F, it might have an issue. If you do not have a temperature gauge, putting a drop of water on the exhaust manifold near each port to see if one of the cylinders takes longer to boilk off the drop of water. This is also where you would want to measure temp with gauge.
As far as the other issues, I would certainly replace the O2 sensor as that can cause problems under load. If it ran good before it sat, I would run a can or 2 of BG44K injector cleaner as gas will congeal quickly and clog injectors causing the types of issues you have.
There are a few other things but the timing issue is important. I realize there is not a lot you can do at this point, butit is something that can be fixed and if there is a bent valve and a cylinder is basically pumping gas through and not burning it you will run into other problems that will get the rest of the motor.
The heads for Hondas are pretty cheap and they are not hard to find.
I would eliminate the issue of a dead cylinder first and move on form there.
Keep me posted if you have any questions.