This is what we used to do. It's not a small job, but if done correctly will prevent future damage.
Remove Rockshaft housing.
Remove Transmission shifter cover.
With filter, sump screen, rear PTO housing(
with bearings & shaft) and all case drain plug(s) removed, flush with diesel or cleaning solution(
non-caustic)(
mineral spirits will work).
Flush transmission lube Cup and Pipes.
Catch flushing fluid in a clean tub/pan.
Flush until clean of metallic particles.
In addition, removed both Final Drives to flush any contaminates. At this time, brake linings were inspected and parts replaced as needed.
If the tractor is equipped with a Reverser or Hi-Low, it will need to be disassembled, cleaned and inspected. Replace any damaged parts within.
Remove and disassemble all hydraulic components(
hyd. pump, power steering, SCVs, PCS(Pressure Control Valve), hydraulic reservoir tank).
Metallic contaminates surely have damaged the Transmission Pump. It will need to be removed and replaced.
While all components are removed, disconnect
all hydraulic lines(
at both ends) and flush with diesel or cleaning solution.
Using a garden sprayer, adapt a rubber tip similar to the air nozzle below.
Flush all lines until clean.
Once you feel all is thoroughly flushed and cleaned. Reassemble with fresh Hydraulic Fluid.