I did my first, of several, auto to manual conversions in stages. I replaced the pedal box first. About 3 weeks later I changed out the tranny and related parts. I seem to remember that the pedal box took me longer to do than the tranny - was my first pedal assembly r/r. If you have all the parts lined up prior to doing the conversion, it goes pretty quickly. The trickiest part of the whole process is making sure you have the correct tranny flange for the end of your driveline.
I've got extra pedal boxes, tranny cross members etc, if you need them.
Cheers!