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MAP fault usually throughs an error (indicated by a flashing MIL). Vacuum in the tank because of a block breather would effect all cylinders. FPR again effects all. A single injector blocked/leaking can effect 1 cylinder and though no faults in the ECU. The injectors all get 12v, so unlikely be the power feed to the injectors but they each earth separately through the wiring to the ECU; they dont all fire of a single feed. Same with the ignition coils - they share the same 12v feed but earth individually back through the ECU, so its possible for the return wires to have a fault but it does run on all 4, just 1 is running cool, which suggests fuel issue, or a stuck valve - as you've already said that you seen in the inlet manifold i'd be looking at the injectors; you could even swap 2 over and see if the the cool running one moves to that cylinder.
 

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when i bought my 954 the guy who had it before me got it from an older guy who rode the bike 7,000 miles and parked it in storage for 12 years. it required a new fuel pump and fuel pressure regulator.
 

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but that would effect all 4, not just making one run cooler then the other 3
Sometimes a bad fpr does show show itself through pistons 1 and 4 even if no fuel is detected in the vacuum hose check. A secondary way to collect evidence against a bad fpr is to start the bike and spray water on headers where they exit the exhaust ports. If 2 and 3 get hot and sizzle the water, but 1 and 4 dont heat up as quickly, it can be because of a bad fpr. Which makes the bike run poorly in turn.
 
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