I know how you feel, I inherited my 64 from Grandad, and Bubba did everything from paint to wiring to brakes. Getting my car up to my own personal standards has cost me 10X what I thought it would.
As far as carb tuning, I got really good advice on this board to start with the basics, ie...distributor performance, is your balancer on right (mine wasn't, what I thought was 12 degrees BTDC was actually 2!) I had some huge vacuum leaks in the intake manifold, I have had to torque, re-torque and re-torque again to resolve. At the end of the day I fixed my driveability problems with simple checks and wound up buying a brand new carburetor I will probably never use.
If I were you I would put a vacuum cap on the bottom intake manifold port, run the vacuum advance to the port just behind the brass bowl level inspection plugs, make sure you have 35-38 degrees at total timing (at 4000 rpm's, making sure your balancer is actually at 0 degrees at #1 TDC) Check your plugs condition, make sure you are not losing spark with Bubba's spark plug wire routing, assuming you have not corrected already.
Carbs are simple devices, and seldom give much trouble. Most driveability problems I have come by are ignition or vacuum leaks, or as a complete surprise to me a balancer problem.
By the way your 66 vert is awesome, I have always liked that blue on midyears!