The welds on the main triangle look fine. Well done!
Those holes in the chainstay are salvageable.
First, if you had any issues with reaching things or gas coverage, make a cradle out of aluminium foil to go around the bottom of the CS, and use more stickout. Before you start welding, just run the gas into the area for a second or two.
Start the arc on anything thick (the existing weld where on the BB shell is probably the best). Be super sure it does start there by holding the tungsten really close to it before you hit the pedal. The arc hitting the thin edge can start to blow it out almost immediately.
Then dip just enough rod (use the thinnest rod you have, I’m assuming 1mm) that it sticks to the weld you already have. Very gently start to build up weld around the ends of that hole first. Only ever point the arc at what you’re building up, not at the edge itself, and always be ready to get rod in there. As soon as you’ve made a blob stick nudge it in the direction you want and get right out of the pedal. Take your time. Let it cool a bit every now and then.
Don’t worry if it looks lumpier than an elephant’s foot. Your goal right now is just to fill the hole. That will inevitably mean piling more metal on top of it.
If at any point the hole starts growing jump off the pedal like it bit you and wait a good 30s before trying again.
Once the hole is closed, you can carefully go over the lumps with the torch again to try to smooth things out a bit. You can even pulse it for some fake dimes (but who are we kidding). But the priority is to have enough metal there.
Finally you can tidy it up as best you can with a carbide burr in a Dremel. Then paint it and never speak of it again.
If in doubt, practice all this first. Weld one of the off-cuts from your chainstays, or something of similar thickness, to a bit of pipe. Make holes and then try to fill them in.
Another option if you’re really struggling and have any of that TIG brazing rod (silicon bronze) is to use that. It will be easier to fill the hole with because it melts at a lower temperature and is naturally quite “filletty”. Although it has less strength than steel it will be fine because the fillet will be quite big. If that works well for you you could even run it over the top of the rest of the weld so it looks like it was meant to be like that 
Finally if all else fails you can always just cut the whole chainstays off, sand back to the BB shell as if they were never there, and modify your design to use shorter ones, or just buy some new ones.
To make sure it doesn’t happen again the advice is:
- Make sure you can see and reach what you’re doing
- Always start on the thicker tube and roll towards the thin one carefully
- Good fit up makes it much easier
