Cat 259d stalls out after 15-20 minutes after getting stuck in the mud

So I recently bought a 2016 259d and got it stuck in the mud . So bad that mud had packed into the alternator. Wiping that out . I eventually got it out. Put a new alternator in it and front crank seal. Now after maybe 15 minutes of running fine I can hear a different noise like a whining noise and the tractor will continuously stall out and then start back up only to stall or stutter again . I changed the fuel filter also . Any ideas where to look next would be greatly appreciate. The stupid move of getting it stuck has cost me over a grand for the alternator etc . So really can’t afford to have the dealer look at it .