I've not changed the filter because it doesn't look any more dirty than the day I brought the tractor home, but I'll change it none the less. My experience with other pieces of equipment and automobiles (some which go 100 to 200K miles without change) led me to believe if it looks clean, it is.
Now that I know what the friction disk is, I doubt that is it. The drop in generator frequency happens very quickly as load is added, and (now here's the key) if I reduce the load, it returns to all OK. On my tractor, what you all describe is very stiff and that often, to move it only a little bit, I must either tap it, or brace my hand against the dash so my movement of it is more measured. I was hoping the disk had something to do with the governor performance, not the throttle setting. On my old Satoh, it had a setting or two that affected how the governor performed. Too sensitive a setting caused it to "hunt" a little but made it very responsive. Too course a setting caused it to not respond until a large variation occurred. I thought maybe the 40D had something similar, but it wasn't obvious by just looking at it. I guess not.
Wally, I have no concerns about stressing the engine on the 40D or any other tractor with a PTO generator unless something is overloaded. I believe several of almost the same kind of engines are used in the larger standalone generators anyway. John Deere even makes generators using some of their engines. These diesels are made to run and run and run. Using the tractor does put the transmission in the middle of things, but whether hydro or gear, me belief is both are well lubricated, cooled, and made to work. I remember years ago, by uncle, a potato farmer in the "thumb" of Michigan, use to set one of his old IH's back by either his pond or stream with a PTO-driven pump hooked up and irrigate those potatoes day and night for several days, often several times a summer. I'm not worried!