1998 BF90 with Commander 3000 Control... Hard to throttle in reverse, cables replaced

This boat is new to me and the cables were shot, difficult to shift/throttle in forward and reverse so I replaced the cables with honda cables and merc adapter. The throttle cable works great in forward and reverse while in throttle only mode, smooth and easy. When I fire up the engine to test, the forward gear and throttle work great, very smooth and easy. Shifting into reverse works fine, however when I try to throttle in reverse while in gear, it feels like something is stuck. Takes a lot of force to throttle in reverse while in gear and also takes a lot of force to get back to neutral. I'm thinking it must be something in the controller since it did shift into reverse and is in gear, feels like something is binding in the controller when throttling in reverse, but only when it's in gear. Has anyone faced a similar issue?

The problem was the cable end on the gear cable, it was too long. After a few hours of taking apart the controller and reassembling like 10 times and testing the action with the cable completly removed from the engine, the cable stop fell out of the holder by accident and it started working as expected. After that mistake, I compared the new cable end to the old cable end and found the new one was 3/4" longer with the adapter screwed in as far as it could go. After taking off 3/4" of threads, it throttles in reverse as it should. It was quite the learning experience.

So, the shifting of the controller works great when the cables are disconnect from the engine now. However, when connected to the engine the shifting sucks! The controller/engine combo is not right and never will be from what I can tell. I have no idea how the previous owner used it for so long like this and wonder how much damage has been done to the clutch. After adjusting and readjusting, I can see now that I have 2 options. Option 1: Adjust it so it goes into forward and from forward into neutral without any problem, but shifting into reverse is terrible and from reverse to neutral also sucks. Option 2: adjust it so the shifting into reverse is better and reverse to neutral is good and into forward from neutral is smooth, but from forward to neutral needs a little extra controller action almost into reverse to fully disengage. Choosing option 2 for now, but it's a no win situation and a new controller needs to be purchases... although I'm hesitant because I'm considering swapping the engine to a mako center console and would need a different controller.