Re: Mercury 80HP / 115HP Powerhead swap info greatfully requested
The "tuners" are exhaust tubes that are used to direct exhaust gasses back into the engine (resonate) to help in combustion efficiency. Direct charged engines and Loopers use them to improve mpg/performance. As I recall the original 3 cyl OMC looper back in 1968 I think it was (Evinrude 55 hp Triump for one was born) 3 cylinders had the exact timing sequence to "tune" the combustion strokes. On 6 cylinder engines, they just used 2-3 cyl tuners That's why 6 cyl "loopers" came to be so fast.
OMC was running 4 cylinder engines too (v4's) and they had a different problem with them. I guess they figured it out because as I recall it got to be whereas you could buy a looped v4 or a cross flow in the same model year... '85????? The Merc midsize 4 (30 hp, 40 hp, and one time or two 50 hp) was cross flow technology even up and into the end of the '90's surely for that reason. Then they kept one of the orig 4 cyl design in the mid range and all the new ones were looped and 3 cyl.
Someone else would have to tell you if you have or can remove and swap tuners.
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Quicksilver 2000 and 3000 control boxes have a neutral start switch but that just goes to the starting solenoid....has nothing to do with run. May be something else in there.
I just spent about 2 hours on the answer to this post and I am pretty much convinced that yhour problem is control box created since you said the engine goes "dead" when shifting, not sputters under the load. Dead to me means that you grounded the CDM's (the trigger modules that fire the plugs).
The 2000 and 3000 control boxes have been around for a long time....maybe back to your engine's model year but......emanating from the engine connector on that wiring harness is a black wire with a yellow stripe. (Don't confuse it with the yellow wire with black stripe which is power to your fuel enrichment solenoid that you use when starting as a choke replacement.) That blk/yel wire is the trigger module ground wire and that is how you kill the engine with the key. The control box grounds that wire when the switch is in the OFF position and that kills the triggers at the trigger modules in the engine.
I have an access port (electrical female pin capped with a removable plug) on my engine wiring harness and you can put an ohmmeter between it and the engine block (gnd) and read an open in Run and Start, and a short in Off. That's the easiest test.
I went out to my engine (later engine design (3 cyl rather than 4 or 6 cyl) and looked at the shift linkage, shift slide, control arm and attachment to the shift rod that goes down to the lower unit. There is no connection between any that and any wiring of any kind. I know your engine is somewhat different, but not that different in that area.
I think your problem is in your control box.
If all of the above fails, then you might: Remove the cables from the box (or the shift cable from the engine and leave the box shifter in the N position) and manually (by hand) move the cables (the shift slide in the engine where the cable was attached) and see if the problem disappears which would locate it to be in the control box.
I think something broke/fell out/wore out or what have you that grounded this wire. The pulse modules are self operating from stator (capacitor charge voltage) and trigger (firing pulse) coils under the flywheel and with the engine at idle, and you not changing throttle settings, changing gears is in no way connected to anything under the flywheel or to any engine wiring. There is no wiring in the lower unit, nor the mid section.
It seems obvious to me that you are killing your ignition, or if your older engine uses 12v to power your trigger modules (not familiar with that, but could) then you could be interrupting your 12v supply to your engine's electronic system......but thinking further, if you did that you either wouldn't get it reconnected every time you shifted, or you would short it out and the engine never would start.
My references are my 1990 service manual and looking at my engine. I am electronically and mechanically proficient but have never attacked this problem.
HTH and good luck,
Mark