Replaced both fuel filters on my 3301 due to coding out, after changing the filters I am still getting the same codes.

[Cliffre01]

The codes are 00087, 00088, and P2294.
The tractor runs for 3 minutes exactly and shuts off, and upon restarting it will repeat this.
It will only reach 1900 RPMs, at full throttle.

What could possibly be my issue?

 

[DustyRusty]

Did you reset the codes? Otherwise, the tractor won't know that you changed the filters. Tractors are not like horses, they don't remember when you work them hard or repair them. Think of the tractor as a deaf mute slave that is at your call and beckon.