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so what is the purpose of these holes?

Rebound bumpers?

With the shorter fork, the 2600# clutch makes sense then. You likely will need power assist to the clutch pedal to use and aftermarket clutch with the shorter fork AND you positively will tear up and twist everything in site.

That is why most every driver car you see will have a reinforced Z-bar.  I'll bet even the light clutch caused the top arm of the bar to twist over time. 

Looking into oilite bushings to replace the crappy plastic ones.

An EBay vendor carries brass bushings to replace the crappy plastic ones.  I've had some in my Shelby for 6 or 7 years and still working good and tight.
https://www.ebay.com/itm/Early-Bronco-Early-Mustang-Clutch-rod-bushing-METAL-PN-EBMCRB/261464757864?hash=item3ce0839668:g:DtwAAOxy3yNTfCNE

Here are pictures of C7ZZ-7528-H NOS Ford service part for reference.  (from VMF post in 2016)

Can you detail what you mean by "steering column shakes"?  Does the column feel loose or is it the steering wheel that shakes?  Any noise accompany it?  Do you have tilt wheel and is the tilt head tight or loose?
Kurt.

You can pull it out leaving trans. end intact.  When reinstalling just rotate a little till the square end slides into the driven gear on the other end.

The speedometer head itself can also be source of needle bounce and have seen damaged nylon gears in the odometer cause it - kind of a "once around" increase in friction leading to speed up, slow down in the movement.
Kurt.

Pretty sure transmission oil migrates in from the lower end but not enough to lubricate the whole cable.  I just remove inner and dip in motor oil.

Sounds like high resistance in the wiring from battery to horn wire or from horn wire to the horns.  Possible spot would be the turn signal connector to steering column or one of the connectors to under hood harness. Could also be dirty or bad horn switch wipers at the back of the steering wheel.
You could try measuring resistance between the cold horn wire and the horns, and the horn hot wire to battery (battery  disconnected).
Also the 67 wood wheel is known to have problems with the horn wires internally where they solder to the contact rings on the back.
Kurt.

Brian Styles theory:

https://groups.google.com/forum/#!topic/shelbyresearch/vvHdD9CG4d0

Like the license plate!

Original TS flasher was connected to the rear of the dash panel near the clock.  Twisted in with a 1/4 turn into a rectangular slot.   Don't know if Shelby changed the factory #224 (blue) flasher as was standard 67 Mustang.  A #323 may work better because of the 3 bulb tail lights as opposed to single bulb on production cars.  Both will twist into the slot.   The 4-way flasher was a heavier duty piece in a metal case attached to the LH side above pedal support.
Kurt.

I've got that photo and it is 3.75".  (too much trouble to post) 

I ended up sealing the entire panel and tail light area with a big gasket cut out of a truck inner tube.
Holes cut out for tail lights and held in the center by the lenses and gas cap.  Top is held to body with double sided tape and the rest just by the tail panel and studs.  ZERO fumes.
Kurt.

If your lid has nuts imbeded in the fiberglass it should have had the screw in bumpers.  Mine look like the one in your photo with a locking nut below the rubber.  Never saw one with the rubber off so can't say about concentric circles.