Brakes on all four tires now the brake paddle is soft?

This is a typical symptom of internal leakage inside the master cylinder. The brake fluid is bypassing the leaking lip seals rather than getting pushed out to the wheels. The fix is a rebuilt master cylinder. If you want to replace this yourself, I have a tip that will let you avoid having to bleed at the wheels.

Which way is the vehicle pulling when you brake? The opposite side is most likely the side where your brake fluid leak is.

Check for leaking calipers, flex hoses, rotted lines, wheel cylinders, even a faulty master cylinder.

Sounds like internal leakage inside the master cylinder. That is commonly caused by running the pedal all the way to the floor during bleeding. Crud and corrosion build up in the bottom halves of the bores where the pistons don't normally travel. When the pedal goes all the way down, the lip seals get ripped on the corrosion. It's okay to go all the way down with a new or rebuilt master cylinder, but with an old one, pretend there is a block of wood under it and never go more than half way to the floor.

These guides will help us fix it

https://www.2carpros.com/articles/brake-pedal-goes-to-the-floor

and

https://www.2carpros.com/articles/how-to-replace-a-brake-master-cylinder

The clue to determining if this is what happened is to pump the pedal rapidly to see if it will build pressure, then hold it but if necessary, ease up on the pressure a little then push harder again. If the pedal suddenly falls away and there's no external leaks or loss of fluid in the reservoir, suspect the master cylinder needs to be replaced.

I wouldn't worry about that just yet. If the brake pedal is moving with little pressure, there might be a lot of vacuum being lost in the power booster with each stroke. The engine will respond just like if it had a vacuum leak but the engine speed should come back down in a few seconds if you hold the pedal down.

Just the master cylinder. I never heard of a bad booster in all my years of mechanicing and teaching, ... Until a few years ago. GM owners have their own set of problems, but for the rest of us, about the only thing that can happen is the diaphragm develops a leak. You will hear the hiss when you press the brake pedal. That opens a valve to let atmospheric pressure in so the engine vacuum can pull on it.

When replacing/repairing the master cylinder, before reinstallation, ensure the seal between the master cylinder and booster is in good condition. The seal tends to fail resulting in vacuum leakages.

If you have the parking brake built into the rear calipers, it's possible they aren't adjusted up yet. I'm not real familiar with Honda's rear disc design, but for some other brands, the rear pistons will not self-adjust out from just pumping the brake pedal like in front calipers. The rear pistons will move out like normal when you press the pedal, but they will go back in when you release the pedal. What you may have to do is work the parking brake multiple times to walk the rear pistons out until the pads contact the rotors. If the cables are rusted tight or you don't trust them, you can use a pliers to work the levers on the calipers back and forth until the pistons come out.

If you have this design, you wouldn't have been able to just push the pistons back into the calipers to fit the new thicker pads in. You would have had to use a special tool to screw the pistons in.

Ensure you have sufficient free play for the handbrake lever. Without sufficient cable free travel, the rear calipers would not self.

1. Was the master cylinder bench bled before installing?
2. Is the master cylinder of the correct size?
3. Is there sufficient/excessive brake pedal to booster free travel?
4. While bleeding the system, was there a lot of air in system?
5. Is the ABS system working correctly?
6. Did you perform bleeding of the ABS master pump? System is under high pressure so be careful when working on it.
7. Does pumping the pedal brings it up and does it sink when pedal is held?
8. Did you check all the caliper slider bolts for smooth movements?
9. Was any caliper pistons difficult to retract while replacing the pads?

Yup. You got what I meant by "working the lever". When you started to feel resistance is when the pistons came out far enough to contact the pads and rotors.

You might consider KHLow2008's suggestion about bleeding the ABS unit. Some vehicles require a scanner to activate some of the valves so the air can escape. This is particularly important if the master cylinder ran dry, or in your case, you replaced it. Here are a couple of tricks you might find useful in the future:

When the hydraulic system is opened, as in when replacing a caliper or brake line, fluid will drain out of the reservoir. If allowed to occur, you will have to bleed the system to the wheel you were working on and you may have to bleed other wheels too. To stop the fluid from draining out, use a stick from the seat to the brake pedal to hold the pedal down a couple of inches. The lip seals in the master cylinder will block the fluid from flowing while you do the work. When you're ready to bleed what you worked on, remove the stick, keep the reservoir at least half full, and gravity-bleed as necessary. Don't fill the reservoir to the top unless you have all new disc brake pads installed. If there are worn pads, you're going to have to push the pistons back in when you install new pads in the future and the fluid behind the pistons will go up to the reservoir and overflow creating a mess.

The second trick applies to replacing the master cylinder but only those that have two steel lines coming out, not four. Crack the soft metal nuts loose so you don't have to struggle with them after the master cylinder is unbolted from the booster. When it is off, use it as a lever to bend the steel lines upward just enough so the fluid doesn't run out. Do your normal bench-bleeding on the new one, then screw the two lines onto it. Finger tight is sufficient. Use the master cylinder to bend the lines back down, then install it to the booster. Loosen the nuts just a little, then have a helper press the brake pedal very slowly so it takes about 10 seconds to go half way to the floor. You'll see air bubbles come out by the line nuts. Snug them up before your helper releases the brake pedal. The pedal should be allowed to pop back quickly. By pressing it slowly, any air bubbles in the lines will tend to stay where they are or they will float back up. By releasing the pedal quickly, the fluid rushing back up will wash the air bubbles up into the reservoir. This will prevent you from having to bleed at the wheels.

For the ABS pump, remove the pump relay and use a fused wire to jump the terminals and make the pump work momentarily. You would know when the pressure has built up sufficiently when the pump noise slows down. Give that a try and see if the pedal increses in height.

For item #3, if the booster push rod had been adjusted out of specs, it can result in the brake pedal being too low.