i recently just replaced my engine in my 94 accord lx. when i start the car there is a slight idle issue but nothing major. its only when i put it in reverse or drive that the idle drops tremendously to the point that its shaking and sputtering like it wants to stall and cut off but when i hit the gas it goes back to normal. what could be causing this issue?

there is a hole in the muffler could that be a factor?

 

Did you just replace the engine 'long block', or did you replace the intake manifold as well?
If the throttle body is dirty or the IAC screen is clogged there may not be enough air flow for correct idle speed.

 

I replaced the long block and manifold. I cleaned the idle air valve and the throttle body and the problem is still there.