I have the same tractor as you MX5200. I also noticed a slight engine tone change after warm up but figured it was normal.
Do you notice an odor change just before the regen kicks in? I can tell when I'm close to a regen by the exhaust smell. Carries smell about halfway through regen period.
What third function valve did you get for your grapple?
Completely normal. My MX5200 does it too.