1975 Mercury 650, ignition, and lower unit help

[Brettgrosso]

So, I bought a 1975 15' Glasply fishing boat off Craigslist has a 1975 65hp Mercury outboard, with all remote controls in tact. Engine did not have any spark, but turned over great! Has good solid compression, and everything else seemed to work great. After doing some ohm testing on the aftermarket CDI switch box and coil, I determined it was bad. So I swapped that out with the stock switch box and coil, from a parts motor I purchased. Started right up! Hurray!! .. until I pulled the lower unit, and changed the water pump, and changed the gear oil, put it all back together, and now no spark again.. WTH?? I also noticed that the shift linkage must not have meshed in the correct position when I put the lower unit back on, so the little push rod that locks to the reverse pin is not engaging. My question is: is there something in the internal shift linkage that cuts ignition power if the transmission isn't in neutral, even though the remote is in neutral, and it turns over? That's the only thing I can think on that changed. So frustrating. Any help would be very much appreciated!!