What are early signs of failure in forks/stem/handlebars?
You are well past the point where I would have told you to throw the bike away and buy a decent one. But IME the frame and fork are usually better built than the components on a bottom-of-the-range bike. There's no real corners to cut on a frame and fork, where they can shave component quality endlessly. Well, they can switch to mild steel tubing but that's rare above the $199 price point. You may well find that the only difference between your bike frame and one on a bike twice the price is the paint.

There's no non-destructive way to tell whether the frame and fork will fail that doesn't cost (a lot) more than the bike is worth. Especially since in this case the bike is worth less than the sum of its parts(1). You could try pulling on the frame/fork to see how flexible it is, but that tells you nothing about how likely it is to fail suddenly (unless it fails while you're testing it). Or you could xray it and have a competant metallurgist examine the images for defects (a single rock climbing carabiner can be thus inspected for perhaps $US200, but a bike is a lot more complex).

If you like the feel of the bike try looking for something similar, probably from the same manufacturer. But looking at their site, you have the mid-range model. I suggest test riding better bikes until you find one you like the feel of. Or do what you have done - replace everything on the bike with better components and hope for the best.

(1) you have replaced most of the components with ones bought retail. So you've paid more markup (and probably labour charges too) than if you had bought a bike with those components already on it. You're probably also suffering from the sunk cost fallacy - you've spent all this money and are reluctant to throw it away. I can't make that call for you, but look at what's left of the original bike and work out how much it will cost to replace it all - especially the wheels. It might be cheaper to buy a better bike and strip the current one for spares.