I run the 2x4 Holley set up on two of my cars. One is my 67 GT500. The other is my 68 GT350 (347).
I can tell you what I do with them. Others may disagree. Power to them?
What I do is get the engine to only idle on ONE carb. The idle throttle positions do not need to be the same on the two carbs. You want the secondary carb throttle as close to fully closed as you can get it.
There will always be some idle flow through both carbs and that includes the secondaries of each carb.
In my view you MUST use a vacuum gauge procedure to adjust the idle. The idle mixture screws do not lean the mixture. They increase or decrease the volume of atomized fuel traveling through the idle slots.
In order to be atomized, fuel must be mixed with air. Thus an air jet and a fuel jet. Those control the mixture ratio.
The a/f mixture is set by the size of the idle air restriction and the size of the idle fuel slot. Those are the "jets". You can't change that mixture ratio.
You can in fact lean the idle by closing down the idle mixture screw to about 1/2 turn, then increase the throttle screw to open a little more.
The reason that you are leaning the idle by doing that is that when you open the throttle you are idling on the mains, which have a leaner mixture then the idle circuit does.
So you are mixing down the idle mixture by using the idle throttle screw.
As far as adjusting the throttle linkage, all that matters is that you are not holding open the secondary/primary throttle with it AND that you want the secondaries to start to open at about 50% of the opening of the primary throttle AND that when the primary carb is 100% open, so is the primary throttle on the secondary carb AND you are not over centering either carb to get that relationship.
In this manner, the two carbs act like a 600 double pumper Holley with a HUGE secondary vacuum operated throttle/booster.
Since the secondaries are going to be opened by engine vacuum/load demand, they really can't flood/bog the engine.
The reason that the vacuum secondary 2x4's were taken out of the road racing cars was that the vacuum secondaries under race conditions had the TENDENCY of not closing the secondaries fast enough.
If you notice, the carbs are mounted backwards. The main reason for that was this is a "street" set up and the primary throttles are centered in the intake as much as can be done.
Some of the small block 2x4's had the carbs mounted forward with the primary carb in the front.
Depending on who you talk to, some think (including me) that this makes a fuel distribution problem in the manifold until the secondary primaries are fully opened.
In Trans-Am racing, the cars were run virtually with WOT all the time. Trust me. If you never actually saw this in person, it more closely resembled death wish racing and everyone involved seemed to be the first one that wanted to die in combat.
If I could post, I'd offer the pile up of cars at St.Jovite as evidence. Death wish.
My small block runs the exact same set up as the 427/428's with the carbs backwards. It simply runs fantastic that way. It's WAY different then my Webers on my Pantera and each is definitely a treat to drive. They put you in a special place and the biggest problem is you can't find a big enough, wide open enough road to drive them like you want to AND you have to go home eventually.
Also on the tuning. You have to get the automatic choke set up operating correctly before you can set up the throttle linkage. If you don't, the choke will have you on too high of a setting.
Best to try to do this with (the choke) with the engine hot. That's where you set the choke to be wide open at full operating temperature. Then you set the choke on "index".
Now bear in mind, that you CAN NOT use the universal HOLLEY choke thermostat. You MUST use the FORD thermostat. These things are marked and they have different opening rates.
The original Ford Master Parts book showed that choke thermostat for the 2x4 FE setup. My SB is using it also. It takes a while for it to fully open. About the same amount of time to heat up the oil +/-.
IF you live in a southern climate of the US, then it probably doesn't matter too much which thermostat you use BUT here in NY, when it cools off, if you use the fast thermostat (HOLLEY being the fastest) you are going to stall the engine which will set off a syndrome of pumping the carbs to start a stalled engine and as a result, you WILL wind up fouling all of the plugs.
Again, trust me on this one, YOU DO NOT WANT TO FOUL up the plugs on the FE. If you were Elvis, you'd take your gun and shoot the car...and it would deserve it too! Mutha effin hore!
OH, almost forgot, it is IMPERATIVE to get the fuel level correct. IF you were an intellectual and did your dual diligence and went to HOLLEY to get the procedure, you're in trouble. You need to drop the level about 1/8" lower then the instructions will deliver you or else, YOU WILL FLOOD with gasoline to the level you will think you hear GOD and think he is telling you this is the "great flood" and you need to build an ARK.
It seems to be related to the ethanol in the fuel? Something about it expanding when warm?
So that's my story and I'm sticking to it. I hope you can find it of some redeeming value?