Missing 3rd on 904 trans

if the KD lever is unhooked from the carb, then the TV, on the VB, should be up against It's internal stop and therefore set to it's minimum pressure. If the governor still has the correct flyweight for 3.55 gears, and is working correctly, then it should build pressure very fast and easily overcome line-pressure to make a very-quick 1-2 shift. Sometimes the shifts follow eachother so fast, that you can almost completely miss the 1-2 shift.
If this is your case;
There are two ways to prove that third-gear is or is-not working;
1) by the tach, and
2) by the rpm increase on the 3-2 manual downshift.
>60 mph with 3.55s, with 27"tires, in Third gear while cruising, mathes to 2650 @zero-slip, could be ~150 either way, on the tach.
> on the 3-2 manual downshift the rpm should jump to 3850 while still cruising, give or take the same 150 or so.

BTW:
With the KD rod/cable removed, the transmission cannot handle any abuse. The clutches and bands will be fine for cruising and light acceleration. But if you start pumping torque thru her, she will slip and soon after, burn up.
If you need to operate in this mode, then you aught to tie the KD lever which is down at the trans, to some position at least half way from when the lever starts resisting your effort, to, all the way back. You still cannot put full power thru it, and the shifts may be late or harsh. The KD is exists, to soften the hits at low-power; that is it's primary function. The further back that you tie it, the higher rpm the trans will auto-shift at, and the harsher the shifts will be.

As for the governor;
The flyweights and springs, come in several calibrations, to match the driveshaft rpm to a desirable auto-shift range, so you can set it where you like it. The driveshaft rpm varies with roadspeed, which at a given engine-rpm, will vary with the installed rear-gear ratio. You gotta tune that puppy to your driving style.
If the 3.55s in there today, are not the gears that the car left the factory with, but the governor is; then, they may not be well-matched. The TV can be fudged either way about one gear ratio, but eventually, it runs out of adjustment range. As far as I have experienced, there are only maybe four flyweights and several calibration springs to service all ratios from 2.94 to about 4.30s. By percent that is about 10% each..... which just happens to work out, very similar to the march of gear ratios, except the 3.73s which are a half-step.
The heavier your flyweight is, the sooner it will shift. You can machine weight off a heavy governor to get the trans shifting in the ballpark, then fine tune it with the springs.
A&A has a governor kit.