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Ok here's the scenario:

I have a '94 RS DOHC. My water pump started leaking, so I changed it...along with the timing belt. When I installed the new timing belt-I thought crank had moved forward one notch, but I wasn't completely sure. So I just ignored my suspicions and continued on. I finally finished, and started the car. I noticed a major loss in power, and it idled at 400. It would accelerate fine if I gave it a little gas, but too much gas would make it sputter. So I adjusted the distributor, and it seemed to act normal.

So now I'm wondering:

Since I screwed up the timing of the pistons and valves...is adjusting the distributor the proper solution, or just avoiding the problem?

As I see it through my night vision.

mechanically, you are always going to be one tooth out.

Being one tooth out tells ECU timing an incorrect figure with distributor in stock location. Adjust distributor to where spark timing is back to 6-14 degrees (pick a number), and spark is back to where it should be, but valve position will still be one tooth out.

So am I putting my engine in harms way by doing this?

Valve/piston events are out slightly from where designed... could cause problems with emissions, and power... shouldn't be any more harm than an aftermarket cam, but I'd still think you are likely to be losing power from/fuel economy from it (even slight) and thus it would be worth to put back to where it should be.