quick thanks to racerone and kimcrwbr1 - finally got a chance to hit the water with my son and launch the old refurbed starcraft today (been waiting for about a month to get the time) and the 1963 Johnson seemed to do pretty good on the water. Starts up, idles and runs WOT.
Only issue seems to be on the charging system and was wondering if you guys had any suggestions on troubleshooting this area - beyond running with a spare charged battery in the boat and only going out after charging on land!

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This is what the symptons are:
1) according to service manual, if charging system working, then I should get greater than battery voltage at the acc terms on the junction box when running at 3/4+ throttle - I am seem to be getting only getting battery voltage, so I think I failed that test.
2) my ammeter shows o amps while running in forward at up to about 3/4 throttle, then meter seems to show negative amps when running 3/4+ throttle and above. I didn't check this reading with my multimeter, was just going by what the dash gauge showed (I replaced old OEM meter that didn't seem to work with new 20amp meter from tractor. Frankly I expected gauge to show negative anytime magnets were electrified (motor in gear), if charging system was not working, instead it just shows negative at 3/4 throttle plus???? Given manual says charging systems turns on at about 3/4 throttle, I started to wonder if I hooked the gauge up backwards and need to swap pos and neg? I didn't try this switch this though as I thought I should run it by the experts.
3) most troubling, I was getting a 'clicking' sound coming from the junction box at 3/4 throttle and above - sound was loud enoug to hear over engine noise from driver's seat.
4) to play it 'safe', I pulled out the charging system fuse from the box to disconnect regulator and this stopped the clicking noise. so I assume noise is coming from the regulator.
*****Any suggestions on how to proceed? Does this clicking sound mean my regulator in the box is shot, but generator on engine my be working?
Again, thanks for getting me running on the water. We (my 13 yr old and I) had a great time and ran the boat for about 45 minutes today and will be going back out tomorrow. Any idea of how long I should be able to 'run' the electric shift system from battery without charging system working (I will be taking a spare fully charged battery and keeping fairly close to home).