Okay, sorry about the questions, just trying to get all the details, It's tough not being there in person.
So I assume the old motor did not have this problem? ?
If adding fuel doesn't help, then it is probably not a fuel issue, or a vacuum leak. It doesn't sound like the Dist. is 180 out, but it could be off. Did you set the timing with a timing light?
Also does it idle good and smooth? And rev good up until 3000 rpm's? Does it cutt out at 3000 rpm's in park, or only cutt out in gear, under a load? Does it back fire(exhaust)? or pop back thru intake?
Check for spark from both coils at idle. At 3000 rpm's only the intrake coil is firing, so it may be bad. At idle both coils should be firing. It could also be a power transistor.
You say there are no codes, do you have a scanner, or did you check codes manually? All do some research and get back to, try to answer the best you can, THANKS, MATT
Yes you are correct about unplugging the coil, and no it won't hurt anything. let me know what happens, I hope we are on the right track.
As for the "Accept", I think you have to login to just answer.
Timing should be 3 degrees BTDC ( before top dead center) @ 550-750 rpms
Here's some attachments that should explain how to retrieves codes. The ECM is under the seat, and has a green and a red LED on it. Ask me anything you need , I'll do my best to answer. MATT