Im not subject matter expert, but i believe these cars have a remote linkage shift assembly.. With that being said I dont believe there is a way to truly get rid of any grinding, other than purchasing a direct link transmission which is a costly fix. Maybe someone with more knowledge may chime in.
-- any kind of troubleshooting I can do here to correct the issue?
Did you also change the clutch line and trans fluid? The day i was having my MGW shifter and line installed was the first time i tried shifting at high rpm and experienced the grind several times. After switching the shifter, line, and fluid i then tried shifting at 7000 rpm several times with no issue! i haven't tried anymore high rpm shifts as i usually shift my car at 6300 so i doubt i will ever experience the grind again but im confident the components changed took care of the situation.
What fluid did you use? Also, did you replace the line with the Ford Racing one, or another brand?
Thanks.