2001 pcm restart issue

-     2001 Sport Nautique by Correct Craft
-     5.8L PCM GT-40 Multiport Fuel Injected, ford 351
-     BLU/BGE, 21.5 ft long
-     Hull: CTC14085H001
-     Engine serial #: 410231 (PLP PRR12 M 410231 1030630)
Problem Description:
-     This is difficult to troubleshoot because it requires running the engine until it gets up to operating temperature and the engine is fully warmed up (with the engine compartment closed).
-     After the boat warms up to normal 160F operating temperature, it has problems re-starting if I turn off the engine. This got progressively worse over the past 2 yrs, and now it happens every time. It will rarely restart, but if it catches will typically sputter out.
-     When the engine is hot, and off, and I try to restart - I noticed that the fuel pump primer relays sometimes intermittently chatter (chic-chic-chic-chic….chic-chic….chic-chic-chic-chic-chic…) after I push the “start” button once to turn the electrical on. This causes the fuel pump to turn on/off intermittently as a result. I then push the stop button to stop this action. Wait a bit and usually that condition goes away after its been cooled off. After cooled off, pushing the “start” button once will allow the fuel pump to turn on for about 4 seconds (which is normal), then pushing the “start” button a second time turns the engine over to run.
-     Commanding more throttle when this situation exists doesn’t seem to help it at all
-     There are times where I pulled the water filter, emptied the gunk out, then re-installed it – it will restart. Probably coincidental because it allows it to cool off.
-     One time I tried to pull the emergency cut-off switch and it seemed to have an issue with running. It could be that there is a bad contact on this switch? But after I played around with the switch for a while, it didn’t seem to have an effect. For this reason, Im suspecting that the problem is more electrical. Possibly with a sensor or with the engine control module. If you notice, the right dash gauge is not displaying (probably just the display LED’s went bad about 5-7 yrs back), maybe that has an effect on it, but likely not.

-     Typically, if I turn off the engine, I raise the engine compartment and wait for it to cool down to below 140F.
-     Once the temperature gauge goes to 140F or below, it seems to start back up fine.
-     Cold start has no problems starting at all, in fact it starts cold every time with no sputtering.
-     If I keep the engine running, there are no problems and it keeps running.
-     The engine performs beautifully when its running.

Whats been tried:
-     Chicago Boat House marine shop tried to troubleshoot. They charged $380 and only replaced the negative cable to the battery, they thought it was fixed but it didn’t improve any.
-     I replaced both relays shown in picture to the right (12 V HELLA relay 4RD 960 388-31)
-     I replaced the distributor cap, spark plugs, spark plug wires.
-     I measured one of the coolant sensors, and it appeared to have the correct OHM reading when cool and when hot.

What has not been tried:
-     I have not performed a full engine tune-up since purchased
-     The fuel filter has not been replaced
-     I have not measured the fuel pressure or air temperature sensor.
-     Its not clear if Im losing a ground to the ECM?
-     I have not traced all the grounds because I assumed that Chicago Boat House did this….

any ideas, thanks in advance

The Fuel pump relay chattering can be a sign of ECU problems. As the power circuit once the ignition is turned on has constant power and the earth from pin 52 on ECU activates fuel relay. It could be a bad earth or a wiring loom/connector problem also. Supplying an earth feed so the fuel pump constantly runs can help you diagnose the problem. (This can be done by grounding end pin on ECC test connector)

This old Gt40 thread has pictures of how to do this and other info that may help.

Checking fuel pressure is a must on the Gt40 if having intermittent problems. The LP fuel pump is a high failure part now at the age of these engines. There are some extra earth points for the ECU on the back of passenger side head. I hope it is something simple and not the ECU.

Take a look through this as well:
http://www.correctcraftfan.com/forum/forum_posts.asp?TID=25584&PN=1&title=poor-mans-gt40-diagnosis