I had the same trouble with the heavy stumble on acceleration. Also had some backfire. Found out the person who changed my motor had two plug wires crossed, and the distributor was out 90 degrees. I was chasing elusive critters like yourself.
Image on top is coil, bottom is electronic distributor. It is very important to find TDC on the compression stroke of #1 cylinder on your motor before you start taking the distributor out.
I did this by using my compression gauge hose without the gauge. I had someone crank the motor and when air surged out I stopped. The I put a pencil in the plug hole and adjusted until it was at highest level. Which then happened to line up perfectly with the TDC notch on my balancer.
On my motor, (separate coil) I pulled the distributor out and lined it up with the cap on to get the #1 pointing at the water pump. (as in first photo) If yours is 2nd photo make sure you have it positioned as in photo. Then I pulled the cap off, (leaving screws loose aids in these steps) as I dropped it in, I pointed the rotor toward the front of the engine. (2nd photo will point towards #1 socket.
see crude line) May take a couple tries, but you will get it. If it is wrong the dist will not seat. Only when its lined up will it sit all the way in the motor.
Leave retaining nut clamp loose for timing. Double and triple check your plug wires. Like I said, I had two miswired. Also may not hurt to check the plugs again. I had 4 out of 6 cracked when I bought the boat. It is a very tight spot to get a socket and extension on these guys. I used the plug socket and a large stubby box wrench to tighten them. (this is all said assuming you have plugs gapped correctly, and are using the correct marine grade plugs. AC delco is best I am finding out.)
Start the motor, then time it. This solved all of my issues. I am having an issue fine tuning the timing because my timing marks are rusted off. But, if you can see yours, your are in like Flynn. You should be back to square one on base timing. It only takes a few hours. If you try to time without checking the basics you are wasting your time. This will however not solve your performance issue if you have the wrong propeller. Achris is hitting that point correctly.