You did pull the shifter right?
The T5 should come apart from the bell without too much fuss. If you are sure you have EVERYTHING disconnected and only the input shaft being stuck is holding it in, use a pry bar and use leverage to get it the rest of the way out. Just be gentle.
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 ****.