200 HP Chase Begins .... Now Completed 14 Months In. WooHoo !!

Dab the nipples and the MAP with white grease to make sure you have a seal. IMO the length of the tubes is not critical but it's your call. Now, a faulty MAP will not let the bike start and run. They go bad. Ask Scott in Exile. Kevin, send him one of the spares I gave you. Ask him if he has extra caps. They go bad and leak. Let's get this Brit Bird going.
 

i can see having those 4 together may cause a problem
if they don't fit good on the nipples then replace
a backfire may blow these off and with lube may increase your odds.
 
i can see having those 4 together may cause a problem
As I think about this, having those vacuum lines piped together could cause the vacuum between the 3 throttle bodies to potentially balance, even when they aren't , giving an inaccurate throttle body adjustment (the throttle bodies could be badly out of adjustment but indicate they are balanced). Hooked up like that could act like a vacuum leak allowing vacuum to transfer from one throttle body to the other. Just a calculated guess having never checked how those vacuum lines for the Cali versions interact.
 
Before you go performing a pile of work, pull one spark plug wire from each cylinder (only run on 1 plug/cylinder instead of 2) and hook up a spare spark plug to each of the unplugged leads making sure each of the 3 plugs is grounded. Start the engine and inspect to see if there is spark from each plug. This will help eliminate the electrical end. If you find one plug not firing it's probably not a software issue but some connection. Troubleshoot that issue. If all plugs are firing, check the vacuum issues next. Lastly I would inspect the injectors. It's very easy to get some dirt in the fuel lines between the filter and injectors which could plug one of them... fixable though.

This summer I rebuilt the 4 carbs on my brother's Honda 90 outboard along with replacing the fuel filter. Put the whole thing together and the engine misfired on one cylinder. I had to pull everything again and found one of the carbs had a grain of sand stuck in the main jet that could only come from me when I replaced his fuel filter. Very easy to happen.
 

Yes that is what i was thinking
 

That sounds like the problem right there. @Gregger @TURBO200R4 explained it. They need to be individually blanked or better removed entirely and blanked at the nipple
 
I got called into work today as several drivers have tested positive and are sick. So I was only able to get a little done. Today I capped off the blue and redid the yellow to the MAP to make sure they are properly plumbed. also pressure checked the hoses for cracks/cuts. Got them looking good. Cranked on the engine and guess what .... NO JOY. still does the same thing. Buggers.
 
Well other things can cause an apparent high MAP reading too.
But let's bottom out on the vac leak.
What are the throttle balance numbers like now?
Would you have a photo or video showing us all the vacuum nipples and tubing etc now?
Would the throttle bodies have been removed or the transition pieces from throttle to cylinder head disturbed during the work done?