GT-40 surging issues

Hi all.
I've got a '95 ski Nautique with the 5.8 GT-40EFI motor. Just recently I started having a problem with the motor surging and bogging down after idling for a while. It's intermittent. It started after I used the boat to tow a small dock a few miles as I was selling an old Harbor Master. I towed it at idle speed basically. When I went to take off it goes fine for a bit, then surges and won't allow me to get up to speed. It doesn't cut out or stop. It sounds perfect when idling when I slow her down. On a couple of occasions we shut her down for a few to look at motor. She then started right up and ran smoothly. If she starts out smooth, she stays smooth. If she starts out surging, she stays surging. I've read a bunch of the posts, but they seem to do better after idling. Help please!
One other note, When I start her in the morning, she typically starts up right away. I've noticed lately that she'll not start cleanly. Don't know if it is related. My thought is fuel related, but maybe ignition?

79, Intake Air Control? Will my motor (which is same as his, but carbed) have this possibility?

Thanks, I'll try that -once I figure out where and what it is! I'll have to do it this weekend as boat is at the cabin.

Thanks again 79. You really are the guru, aren't you? I had downloaded the document earlier, but need to work on it tonight - you know the work thing. Thanks again though and happy turns!