Sounds to me like you have a small leak, maybe bleader washer?  If you run for an hour with no issues that should be more than enough to purge but if you have a very slight leak it would allow pressure to "relax" and possibly give you problems.  Also have you emptied fuel water separator?  I would dry all connections from pump to engine and look for wet after running.  Look close as it may not be very much.  Previous boat I had leak from bleeder bolt,  I could just tell that it was wet but could have dried all up with half a q-tip or less.  Was not much at all but enough to give me trouble.  Also if you smell diesel without opening bleeder or filter you prob have a slight leak somewhere.    Good luck!

Fuel system problems are a Bit** because the system is in series so any fault in the line kills the whole thing.  Can you specify which engine is in your 1994 boat - M35BC?  Many of the "newer" engines (after late-90's) had automatic bleeders where the primary (low pressure) pump would bypass the injectors and return to the tank.  No bleeding needed, like in a diesel auto.

One diagnosis tool I found useful is a 3-foot length of clear 3/8 inch tubing and an outboard motor fuel bulb - a $20 investment even at West.  Rig the bulb in the middle of the tubing, clamp appropriately, and pump some fuel into a milk jug at various points in the line to see if (1) it runs fuel and (2) there are no bubbles in the suction side.  Test the flow just before the primary filter, and just after.

As Matt noted, an hour of running should have cleared out any remaining air, but it returns (or gets clogged) after sitting. Suggest running your fuel feed tests both before and after resting for a day.

You are describing a nasty little problem. It is suspicious to me that when you run the fuel pump you get no fuel coming out of the bleed valve. At least that is how I read what you wrote. I assume that when you do get the engine running, and you then loosen the bleed valve, you do get fuel pouring/squirting out?? If you do, then the problem sounds more like fuel pump issues. On one of my boats, unbeknownst to me, the fuel pump itself had a tiny mesh filter that at one point clogged up and starved the engine of fuel, leading to erratic behavior. 

Related to this issue, I am putting a plug in for adding an auxilliary fuel pump with an on off switch right there at the engine. It bipasses the  regular fuel pump when in use. I love it as I can bleed the engine myself, and if the primary pump goes out, I just turn to the auxilliary. It is cheap and easy to do.

Keep us posted

Al

I had the exact same problem on my C 30. Turned out to be a very small pin-hole in the primary filter that bled off the pressure after a day at rest. Might also be a bad gasket in the filter. Might want to check that. Have you noticed any fuel in the bilge? That's a sure sign of a leak somewhere.