Absolutely no hydrogen peroxide. It destroys the cell membranes of ANY cell, good or bad.

Pictures would be helpful.

Cactus mix is not the most suitable for growing hoyas in, even with orchid bark mixed in.

Compacta actually prefers it drier. I water mine every 10-14 days, and mine is in a mix of 1/4 inch orchid bark, #3 perlite, and 1/4 inch LECA (expanded, fired clay balls).

Did you rinse the old potting media off the rootball before potting up?

I would check the roots first, especially if it is the bottom leaves of the affected stems, that are doing poorly. If the roots and root stem are whitish, firm, smell okay, and not squishy or stringy or stinky, pot back up.

Then, please take a pic of the affected leaves and post here for further help.

I should've known better than to try to get a diagnosis without a picture:)

Here it is:

As you can see, one stem is healthy with green leaves. The other one, not so much. The lower leaves on the sick stem are getting wrinkled and quite soft.

I haven't had a chance to look at the roots- I'll try to unpot it tonight. If there is root rot, how should I treat it? I'm more familiar with succulents than hoyas/other house plants.

As for the soil, I think I managed to get all of the old soil off when I repotted it. I don't really like using perlite- I don't like the way it floats and discolors. Would this plant be happier in just orchid mix? Or orchid mix with gritty mix?

With root rot, unfortunately, you have to cut off the diseased portion of the plant, roots and all.

It would be best potted up in orchid mix ( ot straight orchid bark). If you are adversed to using perlite (which doesn't discolor for me...perhaps you are thinking of vermiculite?), bits of shredded long fiber New Zealand sphagnum moss will work as a substitute. Just cut the moss into 1/4 inch chunks.

I unpotted it last night and the roots actually looked good. They were pretty white (though I couldn't get all the soil off), none of them looked black or mushy and there was no odor.

I repotted it with just orchid mix and I tried to separate them a bit since I noticed the stems were really close together when I potted them last time. It lost a few more leaves in the process (they were pretty soft/wrinkled).

I'm still not sure why one of them has the yellow leaves and the gray spots but I guess I'll see how it goes now.

Use cinnamon mixed with a few drops of water, to make a paste. Apply paste to spots on leaves. Leave on for a day or two, then rinse leaves. Cinnamon is an excellent antifungal.

You thing this is a fungus? Is it likely to spread to the other healthy stem?

I donxt know if it is a fungus, but if it is, the cinnamon will treat it.

I still think it is a root issue, since it is only affecting that one stem. If it were my plant, I'd just get rid of the affected growth, either by removing and discarding that one cutting, or by removing the affected cutting and taking a cutting of the still healthy portions, discarding the unhealthy portions.