Some troubleshooting tips in addition to Ed's document.
I have no experience with Stargazer in short setups. Heaps of room here. I've done a lot of custom systems with PP (inboards, outboards, IO and jet boats) and have a lot of troubleshooting experience.
The factory programmers are very capable. If it was generally the best thing to have a lower baseline, the programming would have been modified by now to do it, and would have come that way in the first place. The suggestion may have merit in short setups but generally baselines should be set as per the factory recommendations.
Ed's boat would be drive by wire, most people needing troubleshooting help would be running mechanical systems.
You need a good earth. Very few ski boats with mechanical throttle engines are wired properly. I've solved many useless perfect pass installations with a wiring loom. I prefer to err on the side of overkill so I run a pair of 6 sq mm conductor size cables direct to the battery. The positive wire has a 10 amp fuse near the battery. An ignition switched relay near the master module takes the 6mm positive wire in and provides switched power for the master module. Very much the same principal as driving lights on a car - you can google that or ask any auto electrician to do it for you.
6 sq mm of conductor size would be overkill and 4mm would be fine too. I use 6mm. Note 4mm CABLE size is much smaller and I would avoid that. I would use at least 4 sq mm conductor size. Don't count the plastic insulation in conductor size as it doesn't conduct.
Servo motor operation should be tested. Use the servo test mode. Ensure no slop is present during any tests. When the servo changes direction, the engine throttle should too. No slop, nothing bending, just exactly doing what the servo does. Some linkages bend as the servo changes direction. Very hard for PP to control speed when the engine isn't even being told the right thing to do!
Test the servo motor operation with the engine switched off at 1/4, 1/2, 3/4 and full throttle. It should be perfectly smooth. I've seen servo cables jump and catch at different settings. Check and fix it.
You may need a return spring. If PP can't get the throttle to return all the way to idle, you need a return spring. Use one as long as you can make fit. Make it only just strong enough to do the job.
RPM modes like classic can compensate better for a poor throttle setup as RPM mode gives PP sample data more than 200 times per second. Stargazer takes into account GPS and I think is a little slower than pure RPM mode to make compensations for a poor throttle setup. Z box is much, much more fussy about this. If your system isn't perfect with Stargazer alone, then it could be a bad candidate for Z box.
For example, a boat was "fine" with Stargazer but with Z box it was giving nasty hits around some buoys. Horrible to ski behind with Z box. Turned out that the blob of glue that holds the string onto the knob on the servo motor was too big and was catching on the string at certain points in the servo motor rotation. Stargazer was so fast it was able to mostly correct for this (nobody had ever noticed it) but Z box mode couldn't. Fixing this took seconds and improved the pull considerably. This was quickly found with the servo motor tests described above.
Another example, I had a chance to visit a customer 3000 miles away and drove his boat. His stargazer was awful. I turned it off and drove by hand and told him it was not nearly right. Hunting, couldn't lock in before the gates, poor times, poor pull, you name it. I built him the wiring loom described above and sent it to him. He told me it transformed the pull of the boat.
When I'm troubleshooting a mechanical PP I do this:
1. Check the servo motor operation as described
2. Check the voltages and or just go ahead and install the loom
Greg