Welcome to FYIFORD.  Glad you found us.

You can run a cable clutch setup with the three speed if you modify the bellhousing for cable.  That involves welding a mounting boss internally to move the lever pivot point to the passenger side, welding a cable stop on the front driver side and using a diaphragm type pressure plate with a Fox 5.0 release arm and bearing.  Personally, I would take the money you would have to spend on that mod and put it towards a T5 five speed tranny and T5 bellhousing that is already set up for cable operation.

Trim the brake pedal foot part so it is a mirror  image of the clutch pedal foot part.

To remove the pedal assembly, you will find it alot easier to get it out if you drop the steering column down a bit, accomplished by removing the nuts holding it to the bottom of the dash and removing the small screws that hold the column to the firewall.  Be careful and check the condition of the rag joint before you do this as it makes the rag joint flex to make it happen.  It is pretty easy to remove the three bolts holding the steering box to the framerail also, and that lets the whol assembly pivot so you can make the column go lower.  You do not have to remove the column, just drop it down.  Pull the seat out if the steering wheel is installed to let it drop farther.

If you want to properly install a booster in your 68, I would strongly urge you to use the factory type booster and power brake pedal.  There are kits that allow a booster to be bolted on and use the existing pedal, but that is a stopgap method to doing the job correctly.  One of the big reasons to install the correct pedal is it has less mechanical advantage and thus a much shorter stroke than a manual brake pedal.  Using a manual pedal with a booster that just bolts on will not give you the shorter stroke and will have way too much boost if the booster is doing much at all.  Parts are available to do it like Ford did it, and that would be my suggestion.  I keep those parts in stock and they do not cost any more than the cheapo bolt-on boosters.

Those 3 bolts in the last pic do not have to come off as removing the 6 nuts from below will let the part held on by the three bolts come out with the pedal support.  But, it won't hurt anything to remove them either.

http://www.mustangsteve.com/fyi_brakepedals/msFAQbrakepedals.html

The automatic and manual trans pedal supports are identical.  I would suggest you install an adjustable clutch pedal stop on the pedal support, as well as my ballbearing shaft kit so you have pedal height adjustability and a very smooth pedal action that will never wear out.  Go to the page linked above and scroll to the very bottom to see a picture sequence showing how to install the adjustable stop.  The stop is included with my CK-167-P kit that has the clutch pedal and quadrant with the cable and firewall brace.