They should be snug against the outlet. They prevent the water from just dumping out the elbows (without going through the engine) at low rpms. Higher rpms/higher water pressure opens the balls and then lets more go out the elbows.
Fill your tank. No way a 5.0 is getting 2 gal/hr.
Edit: was your separator filter dry or have gas in it? As mentioned you have an electric pump after the filter, it shouldn't run unless engine is cranking or running
What's your serial #? An '88 should be Merc manual #7. Your diagram doesn't look right...
Was it overheating prior to your work?
Try running it on muffs and not in a bucket, and verify your temps with an IR gun.
This is the correct area to post.
Spark plug/coil wire, plugs, cap, rotor are the only possible failure points. If you're not getting spark at any plug, I'd guess that the issue is at the rotor button connecting to the cap (I read this as having spark off the coil wire)
The Sierra ones are good, and I've seen a couple of other decent ones. Good ones have a plastic coated inner sheath, pretty obvious if it's quality or not. Electronics, who knows, rubber who knows.
The whole point of the tool is to make sure that there isn't stress on the coupler. If it slides easily, you've confirmed that you're not stressing the coupler. I think the witness marks are secondary, to be used to figure out how to move the engine when the tool won't move freely