Joe,
Have you ever considered replacing the 3-speed with a 5-speed?   It is a huge improvement plus you get overdrive.

I don't think I have ever heard of anyone actually rebuilding a three speed!

Since you already have a manual transmission in the car, you could do it for the cost of a T5, an adapter plate and a driveshaft shortening.  I have the adapters, or you could change to a cable clutch and use a T5 bellhousing, eliminating the z-bar linkage.

You MIGHT get lucky with a $400 Craigslist T5, but probably better to go with a sure thing and have Glen Buzek build one for you.  Say $800... I don't know exactly what he gets for one now.  Add the adapter for $150 and a $80 driveshaft job.   so...$630 to around $1,000 will get you there.  It would transform the car where you would not even recognize the car and the way it performs.  Plus better MPG on your way to the BASH.  What is that, about double what it would cost to rebuild the three-speed?  So it costs you another $500?  Don't forget to apply MustangSteve's LAW whenever doing a mod like this.  Oh, I forgot, you also need a $139 crossmember...  In  25,000 miles, that T5 rebuild vs the 3-speed rebuild would pay for itself in improved mileage.

Joe, sorry, I missed the part about special tools needed.  You will need snap ring pliers, a press - either hydraulic or arbor, and various holders and such for pressing the bearings off and new ones on to the input and output shafts.  And a bushing inatallation tool to remove and install the new tail housing bushing.  You should be able to use sockets at pushing tools for the seals.  And, lastly, a shortened cluster gear shaft - to keep the needle bearings from falling out, because the cluster gear goes into the bottom of the transmission before the input shaft and output shaft and their associated parts.  Then, when the input and output shafts are secure, you lift the cluster gear into position and install the correct cluster gear shaft.  That's the only tricky part of the job.
Enjoy