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Replaced my 4.9L I6 in my 87 F-150 about a year ago and have had this problem since. The engine starts and runs fine when started cold. However, if I run it for 30+ minutes, shut it down and subsequently restart it; the starter lags but will eventually turn the engine over. It will start in this condition. Once started the engine will surge at idle from 1000 to 1200 RPM every 2 seconds. At higher RPM, the problem goes away.
If the truck sits for a couple hours before restart, there is no issue.
My only guess, is some sort of ground issue, but there is continuity from each of the grounding points to the negative terminal of the battery. Anybody got any other ideas?