I have the exact same carbs that you do.  Also have the dreaded intermittent miss especially when engine first starts.  Running a Mallory Unilite with new wires, plugs and pickup.  I have experimented with jet and PV sizes with no real difference.  But the engine runs like a raped ape when fully warmed up (195* thermostat).  If you figure it out I would be all ears.  Good luck.

I think it would be safe to assume that it is a stock type replacement gear (cast).  If it were steel it would be triple the price.  Try contacting the manufacturer to verify.

You will need to change wheels as others have said.  The original tires were 83 series in modern terms (tall and narrow).  The higher the series number the taller the tire.  Going from an 83 series to a 60 series is a big jump in height and width.  Another consideration is the height of the tire and rear end ratio.  Say your car has 3.00 gear ratio stock, going to a 60 series will effectively raise the ratio to around 3.25.  Poor man's quick gear change LOL.

I am running the Unilite non vacuum advance with Accel spark box.  Playing with the initial advance I don't hear any detonation running the engine to 4K sitting in the garage no matter how much is dialed in.  Does get to the point that there is not a miss as such but running rough if it goes too far.  After many years of operating noisy machinery my hearing is challenged to say the least and I may not hear spark knock over the exhaust and other engine noises.  Right now it is set at 16* initial and 38* total but still seems a little rough.  I want the full potential of the engine without doing any damage.  This is a street warrior only so test and tune at a track won't happen.  If anyone has close to the same combination (side oiler, aluminum heads & 2 X 4 intake) in a Mustang and figured out the ideal settings I would appreciate the figures.

Also try to lift the gas pedal from underneath with your foot.  If it returns to set idle something is in a bind from pedal to carb.  Another test would be to quickly stab at the pedal and release seeing if it returns to your setting.  Good luck.

My guess on the blocks would be cost.  I heard that the 427 blocks after casting were fed down a long cooling tunnel to minimize stress.  Others might chime in on this.  Remember time = money.

Watching the Robert Pond interview he stated that he normally shifted at 9000+.  That is the stratosphere for the most of us.  It would be nice to know what the bottom end of our FE's might handle - just the rotating assembly.  There are too many valvetrain possibilities out there so let's just figure crank, rods and pistons.  Say stock 390, 427 and 428.  Then add in some common stroker combinations.  Mine is a 427 side oiler block 4.250 bore and 4.125 stroke with 6.700 H beam rods.
If we can get a ballpark figure for the bottom end then there would be no need to spend extra money on the valvetrain to go beyond the limitations of the rest of the engine.

Welding will "draw" metal and the others chiming in are right.  Be careful of your heat setting on the welder so you don't burn through.  After laying two beads opposite each other, you may be able to use a punch from the bottom on the welds to coax it out of the bore.