OK, you have an NSF/MFS25A. (Nissan and Tohatsu are identical in every respect except the decals). That's triple carbs, as opposed to EFI. Get the Factory service manual (forget the aftermarket manuals). You will want to order Part# 003-21053-0, $40.00, from any dealer, including me. Ignition testing must be done with a good ANALOG meter, not a high-tech digital meter. Your very cool Fluke does not necessarily provide enough drive to the circuit under test to get proper values. Even a moderately-priced Triplett meter will be fine for resistance readings, but getting a meter with DVA capability (such as the ES meter that Tohatsu America sells), is a good choice, and allows reading the ignition pulses going into the coils, without the complexity of an oscilloscope or old Merc-O-Tronic unit.
Seems you are doing fine so far. I can't imaging any hack installing the fuel pump without the o-ring. Based on that work, consider that the caliber of the previous mechanic might not have been what you want. Verify everything. I would suspect a varnished carb or 2, in addition to any ignition issues.
Get a new water pump kit installed. Order 3R0873220M, $37.49. Do not take the "impeller-only" shortcut. A full kit pumps better, lasts longer, and is the same labor to install.
Properly and Thoroughly clean the carbs (there are no shortcuts here):
Remove and completely disassemble all 3 carbs (including jets and emulsion tube nozzles), then soak all non-rubber bits in real carb dip (available at auto parts houses in 1- and 5-gallon cans) for 4 hours at room temp. Then liberally blow out all passages with generic carb spray (you may consume a full can of spray for each carb), and reassemble, paying particular attention to float height. If necessary, get a carb kit: (If you want to do kits in all 3 carbs, you will need 3 kits). Part# 3R3873221M, 55.30 each.
When you reinstall the carbs, you will need to verify the initial synchronization according to the Factory service manual. If that sync ends up being a little off, you can do the "by ear" method (if your hearing is superb), of you can use vacuum gauges and the appropriate kit to get the final dial-in perfect.
Change LU lube, crankcase oil, and filter. Do not use synthetic crankcase oil. Select a 10w-30 or 10w-40 oil that is rated FC-W by the NMMA.
If you see any serious visual damage to spark plug wires, replace them; be advised that the wires come complete with the coil. You don't need to get all 3, but if you have a bad wire, you will be buying 3R0061710M, IGNITION COIL, $49.75 each. If you just need the boot at the plug end of the wire, that's available separately: 3T5069210M, PLUG CAP, RESISTANCE, $21.09 each.
If your serial number is below 062257AX (I believe it is), you need to confirm whether you have had a 5mm drain hole added to the driveshaft housing just forward and above the oil drain plug boss. If not, you can PM me for a procedure to bore the hole. You need that drain if you will ever be storing the motor in freezing weather.
