I know mine is a 4-cyl Fox body, but I did mine for less than $600.
$200 T-5 and bellhousing
$200 Stock replacement clutch (came with throwout bearing)
$050 For all the small parts from a JY (cable, pedal assy, etc)
$030 Flywheel resurfacing
While the pedal assembly is out I would go ahead and put in a St33da clutch quadrant and firewall adjuster, It is a PITA to change while the pedals are in the car. i finally got frustrated and just took my pedal assy out.
This is the link to where I got my info on how to do this. The first time I did this it took me a week. the second time was in only about 6 hours.
When I did it to my first NA 2.3 I used the auto ECU and the only problem was that it spat out a code that the torque converter was not locking out.
I do not know if the EEC-V would react differently though.