This issue has been around for a while, I had the timing belt, water pump, tensioner and all acces belts changed and it did not do nothing. It runs great after it gets over its little problem.

 

Those items could be installed correctly, but the ignition timing could still be slightly off. It needs to be checked with a timing gun.

I just checked the cold start engine idle speed on my 97 Civic (D16Y7), and it was just over 1300 rpm. As the engine warmed, the idle speed gradually decreased to 670 rpm. You may want to rent/borrow a digital tachometer or scan tool to see whether your idle speed is set to spec (see 96-00 Civic manual).

 

Shoot, well I did everything I could do on my own and just payed $350 for the Timing work so now I will have to wait to see where I can take it to have this checked.

 

Well, you might save money by purchasing a good scan tool that measures engine rpm and ignition timing and trying to troubleshoot the problem yourself rather than bringing the car to a mechanic. Just my opinion.