Man, it's been a while since I paid a mechanic to work on my car. The rims were expected, so I'd exclude them from the list, since the amount you paid for the car would have taken that into account.
The nice thing is that you won't have to do these repairs again for a long time.
Did you make a bad decision? I dunno. You gotta look at each thing separately. I'd put them into 3 categories: 1) regular, frequent maintenance, 2) regular, but less frequent maintenance, where the seller chose to sell instead of do the work, and 3) one-time/accidental/fluke stuff. If you're trying to figure out if you made a mistake, then #2 is the category you want to look at
It sounds like the seller sold the car rather than do a bunch of looming maintenance. The good news is that much of that stuff is infrequent/accidental/one-time stuff. You'll hopefully never need to replace any more rims, the brake flush will last for a long time, the spark plugs and coils are good for at least 60-100k miles, and sway bar links last a long time. Rotors and drums last a very long time. Many tire/suspension places offer a "lifetime alignment" where you pay extra once, and you can take the car in for free alignments as long as you own the car.
I think you have a good opportunity to learn exactly how much money you can save by doing your own maintenance. :D Starting from the easiest to the hardest...
Wipers are super cheap and easy to replace, and if you buy a battery at Autozone, they'll install it for you for free, if memory serves.
$214 for an oil change, trans flush, and brake flush? That should be no more than $40 of materials and a couple hours of work if you DIY. The second time you do it, it'll take half the time.
Spark plugs and coils should only run you $200 total, and are right on top of the engine, easy to get to.
Sway bar links? They're like $5 each at rockauto.com. Jack up the car, take off the tires, then two nuts on each side of the sway bar, and you're done.
Brake pads, rotors and drums. Only slightly more work than replacing the sway bar links.
A couple years back, my mechanic told me I needed new brake cylinders in the back and new pads and rotors in the front. The quote was $850. I had never done brake cylinders before, and had only done brake pads once. I bought the parts for $155 and did all the work myself that evening in about 3 hours.