New trans, $1k shipped from ebay, pedal assy, $50-$100, yoke for your DS, $50, shifter $100, clutch $230, flywheel $140. Then there is the computer, you will need it tuned to have all auto features turned off, not sure what that is going to run.
If I were you I'd just do the J-mod to your auto and tune it and go. Get a better converter if you want more performance out of it and still be way ahead of what you'd pay to swap it. I mean you could sell your auto stuff to make some $$$ back but you aren't exactly going to get much.
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 ****.