I remember my three F-150s that had the 4.9 I6 engines (1983, 1989 and a 1992) and every one of them had a slight skip at idle and I was assured by the best mechanic I knew at that time (my dad who was a professional mechanic for better than 50 years) that it was a normal thing for an inline engine to do so, I never worried about it. Still, you also get a vacuum leak warning so it might be time to locate and change out all your vacuum lines. It isn't a difficult or expensive job but getting all the right kinds of lines in the right places can be tough without a road map. I'll see if I have one. What year is your truck?
As to your other issue, it sure sounds like you're getting some water in something that doesn't need or want it! Normally I'd suggest checking the distributor cap but you said it was new so it might be that there is a sensor plug that is allowing water into it causing a short that the PCM reads as an engine issue. If it happens again, disconnect the negative battery lead for about 30 seconds and see if it will start right up. If so, find out what's exposed and fix it, if not, then...well, I'll get back with you then!
Mac
As to your other issue, it sure sounds like you're getting some water in something that doesn't need or want it! Normally I'd suggest checking the distributor cap but you said it was new so it might be that there is a sensor plug that is allowing water into it causing a short that the PCM reads as an engine issue. If it happens again, disconnect the negative battery lead for about 30 seconds and see if it will start right up. If so, find out what's exposed and fix it, if not, then...well, I'll get back with you then!
Mac