If not the bellows, another way water can get in there is if water has collected in the bilge enough to run back through the driveshaft. Remember when pulling up a ramp it might not take that much.
I'm not sure I know what you mean above by the statement in red but please know that no adjustment will fix the problem if the cable is bad. You will have to install another cable, preferably OEM.
The alpha 2 has a system whereby when you shift from forward or reverse into neutral it momentarily activates a switch that kills the motor for a split second alowing an easy shift out of gear. Your cable may be out of adjustment so that it is slightly depressing the switch while still in...
You say you changed "throttle cables". Did you change the lower shift cable? Sounds like you need either a new lower shift cable or adjustment or both. Sounds like when in neutral it's activating the shift interrupt switch.
Is this the cuddy cabin version? How is the boat stored? Not to insult your intellect but could the front hatch be leaking and water is collecting in a front compartment and running back when transom is lower? Buddy had a 94 Crownline do this.
My 2002 5.0 MPI did this on cold starts. The fix was changing the IAC muffler. This happened before I learned to use the internet and forums like this. Remove the flame arrestor and look where the passageway goes toward the IAC. It stuffs down into a small opening. It's a fibrous foamy...
On my alpha 2 it's located right close to the shift interrupt switch which is attached to the shift plate that's attached to the starboard exhaust elbow. Sorry don't have a pic.