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I've been having intermittent slow crank problems with my early 99 F-250 4×4 for some months. It took me a while to figure out that my problems were related to a slow cranking starter, but now I've learned to recognize the sounds associated with a starter not turning quickly enough. The telltale clicking the injectors make when the engine is not cranking fast enough an is not going to fire. I had a failing starter selenoid and ended up having to replace the starter in a hotel parking lot last month. I had the guy I was with disconnect the batteries and clean the terminals while I was underneath the truck swapping out the starter. With the new starter it cranked like it should and fired quickly, for a couple weeks, then went back to cranking slowly and barely starting. I I checked all the connections and discovered that my friend had done a poor job cleaning and connecting the battery terminals. I cleaned them and fully charged the batteries while they were disconnected. I reconnected them and it went back to cranking like the wind and firing quickly. It worked great, for about a week....

Now, it's back to cranking too slow and barely starting (or not, if the overnight temps are in the 40's and I don't plug in the block heater) but this time the symptoms a different. Now the starter increases speed gradually until the engine starts. The thing that has me puzzled is a strange clicking/knocking noise during cranking ONLY when the engine is warm. It's different from the clicking I've come to recognize as the "it's not going to start, stop trying before the batteries are dead" noise. I believe this is a different problem. It cranks the same when cold, but the noise is only present when the engine is warm. I'm at a loss. I'm going to recheck and clean all the connections all the way down to the starter and check/charge the batteries again. I'm not sure what else to do. Any input would be welcome, thanks.
 

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I'd be suspecting the starter itself. If everything else checks out, check out the starter, beginning with ensuring the mounting bolts are tight. That's the ground path for the current going to it, and if it's intermittent, that could explain the noises you're hearing.

In checking the cable connections, do not neglect checking the ground cables. EVERY connection in a circuit counts, and a high resistance on the ground side is just as bad as one on the hot side.
 
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