Changed brake pads. Now my car is periodically difficult to stop and brake pedal gets soft.

first replace master cylinder the replace rear wheel brake cylinders.. Inspect front pads for non uniform wear, inspect front rotors replace if badly worn or scarred. You are dealing with 23-24 year old parts.

Try bleeding the brake sys

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I would jack up a front wheel and see if pushing on the pedal with the engine running will stop the wheel from turning.
You need to know if the pressure is reaching the wheels, or if the pads and rotors are too slick to stop the car.
Usually if the pedal is hard, the booster is not working or the brakes are glazed.
Can you stop the car with the parking brake ? That only uses the rear brakes.
You may need a second opinion from a different shop.

You will need to bleed the brake system. I would start with the rear brakes lines and work towards the front.You must have key off engine off when bleeding brakes, apply pressure on brake pedal 10 times and hold. The brake line is now ready to be open. Open and let the stream of fluid come out and close the line tight. Then release brake pedal once bleeder screw is close. This procedure must be repeated twice front and back. After, brakes have been bleed pump the brake pedal before putting in drive.
Note: Don't let the resevoir run low on brake fluid. This will cause air bubbles to accumulate on the brake system. Always top off before opening bleeder screw.

it sounds like there is still air in the brake system that has not been removed.you don`t say if you replaced the brake pads and shoes(in which case you shouldn`t need to bleed)or you replaced a brake line(s) or wheel cylinder or caliper.you will have to keep bleeding the brakes all 4 wheels(trucks don`t use bi-directional braking meaning right rear brakes with left front and so on).bleed both rear brakes then bleed both front brakes,was this problem there before you replaced the brakes(soft pedal noticed) and this is why you changed the brakes or the pedal was soft and the brakes needed changing.its possible that the master cylinder has an internal leak and may need replacing.

The problem is not the booster, the job of the booster is to make braking easier. If the booster went out the brakes would be hard to press.
Your soft pedal is likely due to air in the brake lines. Bleed the brakes and go from there.

bleed your brakes. new pads always take time to break in. Everytime I change a set they are never as good as the ones I replaced until after a little break in period. Do you have a high pedal or low pedal?

Actually, changing the front rotors is not that difficult and they are relatively in-expensive. Anytime you change the pads on the front of your vehicle i would recommend having the rotors resurfaced or replaced. Especially if you are getting a brake pedal pulse when applying the brakes. Here is a step by step guide that will help you in removing your Front rotors.

Because of the ABS system if you press the brake pedal with too much pressure then it will give you the illusion of a soft pedal. Does it feel like a soft pedal when the vehical is in motion and you then press on the brake pedal (normal)? The other thing is if your pads and/or caliper were frozen, when you changed them out. The brakes are not going to feel or brake exactly the same, after the repair. But you are there, if the pedal is real low or goes to the floor then there is still air in the system or for some reason, your master cylinder is defective.

are your rear drums set up? why did you bleed the brakes. when only when you installed new pads?