Soft pedal after conversion.

.anyone have any advise on how to solve this problem?
Yeah. this is a two-parter
Part-1, hydraulics
Take the wheels off, and remove the calipers. Go get a pair of big iron C-clamps and clamp the pistons into the bores, all the way down and hard. Hang the calipers up so the lines don't kink.
Now go step on the pedal. It should be high and hard; No Exceptions. If it is not, and it is still spongy then one of four things is wrong;
1) the rear drakes need adjusting.
2) there is air in the system, or
3) the flex hoses are chit.
4) the reservoir is plumbed backwards.
Well I suppose
5) the master could be leaking internally.

From the easiest:
A) With the C-clamps still installed; pump the pedal three times in rapid succession coming all the way to the top on each stroke then, on the last pump, keep the pedal down hard and hold it there, at a fixed amount of pedal force.
If the pedal slowly sinks, one of two things is wrong ;
1) there is an external fluid leak, or
2) there is an internal fluid leak inside the M/C.

B) If the pedal does Not sink, but is still spongy, check the plumbing. Your system should have a Brake Proportioning Valve. The rear-most reservoir should be plumbed to the top of the brake proportioning valve and from there it should split to the left and right sides of the car, ending at the flex hoses and calipers. The other reservoir goes to the rear brakes, making a pit-stop at the P-valve.
If this is how you are plumbed, proceed
C) check that your Flex hoses are not absorbing all the pressure by blowing up like balloons. then proceed
D) readjust your rear brake shoes hard against the drums. stomp the pedal to re-center them, then adjust some more as may be required. But before you start, make sure you understand how to loosen them later, and that there is a physical portal thru which to work.
If there is not then STOP!
E) Instead, take the drums off and all the brake hardware, then go get two more C-clamps and clamp the pistons into the bores in a manner that there is no way for them to fall off. Clamp them flush to the rims of the bores. Now go check the pedal! Right now, these hydraulics are fully locked, and the pedal should be high and rock hard.
If it is not, the only possibility left is that there is air in the system. There is NO OTHER OPTION. and
my guess is that the air is in the chamber between the two power pistons in the M/C.
F) You did bench-bleed the system right? and
You understood what you were doing right?

Part 2, mechanical
In the unlikely event that your hydraulics are 100% Ok,
Well then, lets look at the mechanicals.
First the mustbes
1) the Metal pad backer mustbe dead-flat, and the face of the friction material mustbe parallel to the metal backer.
2) The installed brake pads mustbe parallel to the rotors in every plain.
3) the calipers mustbe able to advance freely as the pads wear. So; no bent pins, no divots in the brackets, pads not sticking in their ways; whatever system is used, the pads must be free to advance and free to allow seal-retraction, to pull the pistons back.
4) the two faces of the rotors mustbe parallel, within a couple of thousanths.
5) the faces of the rotors mustbe perpendicular to the axis of the installed bearings, so that the installed rotors have as good as zero runout.
6) the wheel-bearings mustbe adjusted to not allow the rotors to wobble as they turn.
OK
so, now the whys.
Most of those mustbes will be just fine. The thing that you are looking for is a pad that is not sliding tight to the rotor, and so, is acting like a spring; or a caliper that is somehow wedged at an angle, and so has to be hydraulically forced into alignment. Either of those situations will cause a sponginess and a delayed brake action, that usually manifests as a pull, especially in light brake applications.
If your system has a separate caliper mounting bracket, then it, or the mounting of it, is likely to be the principle trouble maker.
Sponginess can also be caused in the rear brakes, but since the w/cs are clamped in place, that rules out ALL of the rear mechanical system.
Also in the mechanical system; I should mention, that if the sponginess went away after the rear w/cs were clamped, then you might want to check that your park-brake system was fully released and the cables relaxed and that the brake arm was fully parked, thus relaxing the strut.
Also, FYI
the star-adjusters are "handed", as in mirror-imaged from side to side. Sometimes if they have been flipped side for side, the adjuster wheel ends up in a hard to adjust place.

Ok so what did I miss.
Oh yes
As for the Combination valve. Inside the valve, is a shuttle valve that separates the two halves of the system, ie the front and rear halfs. The purpose of the shuttle, is to ground out the Safety-warning lamp, if one or the other side suffers a catastrophic fluid loss. It does this be being shoved towards the failed side by the still-functioning side. AFAIK, when the shuttle moves over, it also shuts off the fluid in the failed side, at the valve. The shuttle is supposed to be self-centering after the repair is made. And I'm sure when new, they are/were. But does that guarantee that they still are today.
Unless you installed one, your 65 does not have a brake-failure warning lamp on the dash. So then to see if the shuttle is centered you're gonna have to check it for continuity to ground, which can only be if the valve is off-center. You test from the brass body to the electrical terminal. To move it, you gotta open one side of the system and move the shuttle hydraulically using the brake pedal. There is no way to know which way to move it so it's trial and error.
OK, Happy Hotrodding.