My engine in surging whenever I get around 1800-3000 RPM. Once it's up on plane past 4000 RPM it runs great for the most part. It is a '98 200HP Merc EFI. Originally I thought it was fuel related and I checked the fuel-water separator filter and the in-line fuel filter (both were replaced back in April 2017 and still look perfect). I checked the fuel to see if there was any water that got in, and it looks good (I use Quickleen and Quickare every tank). I checked the thermostats to see if maybe they were clogged or not working right and they look fine.
Once I accepted defeat I took it to a mechanic and had him go through the fuel system and replace the lower unit seals (needed to be done anyway). He found that there is an elbow fitting just below the fuel pump housing that went bad (common problem for these motors) and was allowing gas to siphon back up into the oil reservoir on top of the engine. He fixed that and we were hoping that would fix it... when I took it out to the lake it got up on plane with no issues, but the problem came back after I tried recreating the issue again.
My mechanic met me at the lake so he could see first-hand what the issue was and he also brought an ECU he had in the shop that he knows works so we could test to see if that was the problem... it wasn't and didn't change the performance. He thinks it is a couple of cylinders cutting in and out instead of fuel. However, it doesn't happen every time (maybe 3 out of 5 times getting up on plane). He mentioned that it is difficult to diagnose these type of issues and the first recommendation was to change the switch boxes. I replaced both switch boxes and made sure all electrical connections were sound. It seemed to help slightly, but it is still surging.
His next recommendation is to have the fuel injectors cleaned, but I don't want to just keep paying to replace/clean things if that isn't the issue. So before doing that, I wanted to turn to you guys first to see if you have ran into this issue before and have any suggestions.