What could be done to make the heavier quarks(strange, charm, top, bottom), positronium, protonium, neutronium and other kinds of subatomic matter to be stable and useful?
There's a whole raft of different questions and assumptions in there, but lets focus on the two key ones.
Firstly, things decay or transmute for different reasons. There's not one "decay force" that you can manipulate to control the process. Some, like positronium, can't ever be stabilized... that stuff is inevitably going to annihilate, because the wave functions of the consistent parts overlap which means they're inevitably going to collide with each other and annihilate no matter what you try.
Others decay as a result of various interactions with fundamental forces. If you could manipulate the weak force somehow, you'd be able to render a whole bunch of things stable (and conversely, render some stable things much more unstable... useful if you were trying to make a fusion reactor fueled with 1H, for example). Things which decay due to electromagnetic interactions (like neutral pions) wouldn't be affected by your weak force magic, and so you'd need a whole different kind of magic to control the electromagnetic interactions, and so on.
The next problem is making these things useful. There's no guarantee that any of this stuff is useful. Sure, some of it probably will be... there's all sorts of interesting possibilities if you could stabilise muons and make muonic matter which will be much denser than regular matter (useful for shielding, or mirrors for far UV perhaps) and have a whole new kind of chemistry. What there isn't is any sort of guarantee for merchantability or fitness for any particular purpose. What you've ended up with is a magical technique for making magical materials whose properties are pure handwavium.