I have a 1988 Ranger 2.9 manual trans that I have been working on. The other day in a big rain storm, I hit a puddle, after which it almost died. For the next few days it will start fine then hesitate once you get into 2nd gear. Sometimes it will run for a while then when you come to a stop, it will hesitate for a minute, then it will take off like it finally is getting enough gas. When it starts to hesitate, it is still running, it is just like it isn't getting enough gas or air. I've changed out the PCV valve, checked for vacuum leaks but still not sure what is wrong. This has happened twice. After the first time, it just started working fine after a few days without rain. Anyone have any ideas what it could be?

 

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First I would change the fuel filter(every 5 years) and while under there I would check the wiring on the high pressure fuel pump in the frame rail, it was an add-on for fuel injection, so wires are spliced into the original wire going to in tank lift pump.
That splice did cause problems as wiring got older, and the rain means under side of vehicle is being constantly being bombarded by water, so wires are moving more than in dry weather, with just air flow.

One wire on the pump will be a ground, sometimes it is spliced and sometimes grounded to frame.
The other wire is for 12volts and will be spliced.

The 12volt wire only has 12volts for 2 seconds when key is first turned on, after engine starts it will have constant 12volts.
Block wheels, start engine, move wires around with you hand, see if engine stumbles or stalls.

Also do the same thing with wires under the hood, wheels block engine running, move wires around