New Engine, Same Problem (400 Cummins)

A little background info, I have an early 90's Kenworth log truck. It's a self loader so it has a pto that turns a hydraulic pump which runs the log loader. The truck had a 444 in it until this summer when it dropped a valve plus had some other issues. Rather than rebuild that engine I had a 400 cummins built. Everything on the 400 is new/rebuilt and no parts came from the old engine. So here's the issue, randomly the engine will start idling high, around 1,000 rpm and won't come down. It runs just fine when it does this, it just won't return to normal idle speed. The old engine did the exact same thing. There's no rhyme or reason to it, and sometimes it will return to normal after a bit of highway driving and other times it will run like that all day. It always returns to normal the next day though after being shut off and cooling down. All the fuel lines are new too. I took it into a mechanic a month or so ago and he said something about the PT pumps sometimes sticking or hanging up or something like that. I was hoping someone out there has some ideas on this. It doesn't affect the performance or drivability of the truck but it is annoying. Lastly, I have cleaned/lubed all the throttle linkage and pedal and I don't believe anything there is rubbing or sticking.

 

Floormat is clear of the pedal and I've cleaned out any dirt from around the pedal. I've also cleaned/lubricated the hinge pin on the pedal.

One thing I forgot to mention, and this was true for the old engine as well as this new one, is the engine speed after running the PTO. When I run the PTO/loader, the RPM's are maintained at 1,100 with an electric solenoid in the fuel system. I flip a switch and the RPM's go to 1,100 and stay there until I flip the switch again. Anyway, after running the loader for typically 30 - 60 minutes, the engine will stay at 1,100 even after disengaging the solenoid. It does come down from this eventually, usually to 800 or 900 but does stay up there for awhile. This makes me think there's something going on with the pump but it's just so weird that both engines are doing the same thing.

 

Yes, it has the TR 1001 governor and actually, this was the ONLY thing swapped over from the old engine. Is it possible for this to partially engage and run the rpm's up less than what it's set to?

Here's what happened today:

Ran the truck for about six hours, loaded/unloaded one load of logs plus about 150 miles of highway/town driving, no issues. Stopped for fuel and shut engine off for fueling, started truck, still running normal. Drove about 15 miles on the highway, flat ground cruising about 65. Came to the next town, put truck in neutral when stopped at red light and was idling about 750 (normal idle is 650). By the time I got through town it was up around 800. Drove another 45 minutes to the next town and it was still up around 800. Put another load of logs on and engine stayed around 1,100 after disengaging governor. Drove about 10 minutes back to the highway and idle had gone down to about 800 or 900. Drove home, about 90 minutes and truck was idling at 750 when I shut it off for the night.