I have had something like that happen in the past and it was an injector not connected properly (aka, no good connection).  Also, the rubber elbow on the auxillary air valve, if in poor shape, will make the engine want to die.  The cold start injector could be injecting fuel when it shouldn't be.  One or more spark plugs might not be getting their fire.  I have had a wire come out of the connector to a plug...screwed it back in and drove on.  I might guess at least one cylinder might not be firing if you feel the engine is unbalanced and you feel a reduction in power while running.
What else? :-k

Do you set valves with hydraulic lifters (assuming that Neptune still has the hydraulic lifters) in the same manner you would if you had solid lifters?  I know there is supposed to be a procedure for adjusting the valves with hydraulic lifters, but I don't have my book in front of me and its such a long walk to the garage.

Wow!  A single thread with references to Bus fuel injection AND hydro lifters! I can't believe someone hasn't offered a suggestion of junking the whole lot for a carb and solid lifters. :roll:

Unless you're getting that banging sound when you start up that says you have a deflated lifter, start looking for the injection issues mentioned above. I'm not the one to ask here since I'm the one that gave up and threw on the carbs! Check everything rubber for cracks-just one little air or vacuum leak can make those symptoms!

 Keep in mind that the weather may just be a coincidence. Remember when I filled up the tank of the Sebring in Trenton going to the Montgomery show? My idle air control solenoid failed at pretty much the same time, causing the car to stall at idle-the same as if you get a tank of bad, watery fuel! This failure had nothing to do with the fuel, but I went in the wrong direction trying to fix it for weeks assuming I had bad fuel.