is this possible these motors were supposed to be upgraded to 565 hp could someone muck up the program and eliminate entire cylinder; would no. 3 just be the leanest cylinder. he also ran these motors all summer .

Did you confirm lack of spark or fuel ?

yes there is spark ,hard to with the fuel ,plug smelled of fuel,but wasnt wet.

if everything checks out ok good compression,fuel psi,injector getting signal from ecm,i would pull the injectors and have them flow checked and cleaned,we offer this service 25/per injector,what we have also seen on the 500 injector is when they get old they don't like the fuel psi too high,at around 50-60lb they quit firing,when new they seem to be ok at 50-60lb,now the 500efi is set at 32-42lb psi at the factory but if the filters in the cool fuel get clogged or the fuel psi has been turned up the psi could rise resulting in an intermitting firing injector,if you need any help or your injector cleaned give me a call Dave 410-956-5381

May want to start it without water, manifold or header leaks can cause a cylinder not to fire when it has fuel and spark. Odd both would do it but I don't think anything in an ECM tune could cause it. Assuming firing order and all connections are ok.

yep....rusty exhaust valve wont seal....

You could always switch injector with another cylinder and see if the problem follows. Seems odd that it is both the number 3 cylinder.

or take the guess work out and do a compression check and or a cylinder leak down check

We verified spark, cylinders have 125 psi.Tested the injectors and they are pulsing, wether they are spraying fuel I cant tell. Plugs are clean as the day I put them in the rest have all fired. Put new caps , rotors and tested spark plug wires for continuity. When I pulled my headers which are brand new from lightning, the number 3 cylinder tubes from both engines were clean no carbon no discolor never had exhaust thru them.It doesnt make sense other than the ecm has them programmed out or 2 bad injectors at the same position on both motors. I have the boat at Real Fast Marine in NC to have them check it out plus some other work on it so waiting to find out what the problem is. Worst case I put intakes and carbs on it and take care of the problem

Something you might want to check is cam firing order. Could it be a 2-3 swap?