When you set up the cable did you check to see if the throw was equal in fwd and rev? When I did mine not only did I have to do the transom shift cable but I had to do the remote cable as well. Did you start with the shift rod height adjustment on the lower unit? Everything hinges on that, if this is off it will not be right no matter how much time you spend on the other adjustments. Then, did you measure the cable drag, with the cable disconnected at both ends? Less than 2.5 lbs with a fish scale? That's the other critical thing. When I did mine, with the transom cable disconnected at the engine bellcrank, (ENGINE OFF) I shifted it in and out of gear with someone spinning the prop and marked on the cable itself, how far it was from neutral to fwd and neutral to rev. Then when I hooked up and adjusted the remote cable, I made sure it was the same. If not either the remote control is worn out, or the remote cable adjustment is still not right. They are not that hard to get right if you get the shift rod height right and have a good cable and control. I did mine in 2013 and its been great ever since. Before that, the last time it was done was 11 years before!. I only had to do it because the remote adjustment changed. So I went back and re-did all of it.
PS, I don't think I'd trade a good running Cobra for an Alpha. I like being able to change the water pump in 5 minutes, and having a bellows that is not a battle to change. And OMC's shift assist system, is superior. It does not stall the engine like Merc's can as long as your engine tune and idle speed are right. Yes it is hard to find mechanics who know them, but if you make sure all those points are covered, it should be good. I suspect your control, cables or remote cable adjustment. Keep in mind that the Alpha is not so different, its dog clutch shifting in the lower unit, with a 2 cable system. Same basic idea.