Manual Transmission Advice.

I have similar power but a heavy 68 Barracuda FB @~3440# empty. Ima guessing you're running a 280*cam or better, and a chitload of cylinder pressure.
That combo is not really happy with a 2.66x3.23 =8.59 starter gear. 800 rpm in first gear translates to a minimum speed of 7.5 mph. At low rpm (Just off idle) it will be very jumpy and the more timing you throw at it, the worse it will be. So yur parade-days are over.
I know of just a couple of cures for this jumpiness
1)retard the idle-timing
2) Install waaaaaay more starter gear
3) slip the clutch
4) install a dash-mounted dial-back ignition timing device.
I had to do all four and it was just barely enough

I run the 3.09 low Commando box, with a 3.55 in the back, for a starter gear of 10.97.
And I run 12 to 14 * idle-timing
And a 276/286/110 cam (at .008 tappet lift)
This engine will idle down to 550 rpm in first gear with the dial-back taking out timing. This gets me to 4mph, and the engine will pull the pig around, on a flat,level, hard, surface, without any help from me. But any slower and it gets jumpy again.( yes it will idle down to 500, but I gotta put some toe on the clutch pedal).
I use a CenterForce diaphragm but not the CFII disc; I found it too harsh. I run a standard 340 disc. The CF used to rip the spring-retainers and throw out the springs of those factory discs until I reduced the static pressure. Now they do ok. At higher rpm the flyweights move out and take over the clamping.
So to recap my picks;
CenterForce diaphragm with NOT the CFII disc
Commando box with the 3.09low
3.55s minimum, unless you're a heck of a tuner then 3.23s but those are all wrong for this manual-trans combo.
Short-handled shifter
rev-limiter

Additionally;
That Commando box AFAIK does not come with a slip-yoke output; so you are gonna need to get a 67 up output shaft and a67up slip-yoke rear tailhouse.
That means the trans has to be almost completely torn down. Since this is a given,
Here are a few suggestions;
1) That trans IMO was never designed to be shifted where you are gonna need to shift it at, with a 280* cam. So to shift at 6000 plus; I would
street slick-shift second and third, second at the very least; and modify the cones to cast off their fluid faster. Run a 50/50 ATF/80-90EP oils
2) I would convert to a longtail, and
3) I would put the shifter back between the buckets, next to your thigh; then there's a good chance you will never again miss a shift
4) the trans-end levers absolutely have to be loctited on.
5) you are gonna need a rev-limiter
6) I hope that engine has had the oiling mods done, so it can survive at over 6000.
7) ball. The only kind of shifter handle to use is a ball. Do not install any other kind of shift handle; you'll probably be sorryyyyyyyyyy,lol.

Ok so why the 3.55s for a minimum?
Well if a 280* or better cam, that sucker will power peak around 5600 rpm... which will want a 6000 shift. With 26.5(83.25rollout) tires, this will be about 47mph with 3.23s and a 3.09 low. On the shift, the Rs will drop to ~3730.... so your combo better be making some torque down there.
To overcome this split, I rev the snot out of mine and drop in around 4400 for a good pull to 60mph.
But with 3.23s this pull ends at 60=4720. With 3.55s it ends at 60=5200; still not great but that's the way it is.
Anything more than 3.55s and you will soon be wishing for an overdrive.

In conclusion
I highly recommend to keep the automatic,but make it a 4-speed auto, with overdrive. Then you can run whatever gears that the 280* or better cam, wants. Like 60=5800 in second, which with an A500 would be, like, 4.88s,lol............ 65 in od would be 2770. With 3.55s and no-od, it would be 65=2930
' course the 4.88s were just a suggestion......... I guess 4.56s could work too,lol
I ran 4.30s for one summer, with a manual trans and an overdrive of course; First gear was pretty much useless with the 4.88s,as it was an extremely low starter gear.