Classic 3650 shift fork issue. Rebuild with all the TSBs done or get a new one. You can get a brand newly rebuilt one to your door for $1400 including the core charge.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.