Welcome to the forum!
Sorry to start on a bit of a downer, but it's a bit of a shame that you already installed the speaker wire in, unfortunately, the wrong spots
Speakers for a home theater setup do not go in the corners of a room, and ceiling positions are basically a "last resort" when you have no other placement options. What you would want to do, ideally, is follow the recommended speaker positions suggested by Dolby , which are the standard that is also followed by THX, DTS and any other home theater audio companies.
So you might simply wind up not using the speaker wires that you've pre-installed, which is a bit of a shame since you went to the effort, but not the end of the world
I'd certainly sooner have correct speaker placement than shove them into the upper corners and detract from the sound quality simply because wires have been pre-run to those locations
In terms of what you get from a HTiB, Onkyo, Denon and Yamaha all offer fairly decent all-in-one package options that at least give you a real receiver and some inexpensive, but functional speakers. The biggest problem I have with any HTiB though is that the subwoofers are really sub par. While it's obviously important to have a good center speaker for all of the dialogue and good Front L/R speakers for all of the music and effects, the subwoofer is what really makes a home theater sound and feel like going to a full sized movie theater! You do NOT want to skimp on the subwoofer!
The surround speakers are the least important. Surround effects are meant to envelop the audience and create ambient sounds and only the odd, distinct sound effect. In truth, if you want to recreate the same surround effects that you will hear in a movie theater, the surround speakers are meant to be placed 2-3 feet above the height of your head when you're sitting down. They're meant to be directly to either side, or just slightly behind your seat, and firing across the room's width overhead - ie. the two surround speakers are facing each other, and not aimed toward the listening position. So if you're going to skimp anywhere, skimp on the surround speakers, for sure. You can use super inexpensive speakers like these $28 bookshelf for surrounds and they'll do just fine
TheInfinity Primus speakers are definitely an excellent suggestion for inexpensive, but very good speakers for a small room like yours. You don't have to buy directly from the Inifinity website. The Primus speakers are even less expensive elsewhere. For example, Amazon sells the and the matching for $150/pair ($75 each).
So that's about $330 (if you use the very inexpensive monoprice speakers as surrounds) for 5 speakers. And that's good because it gives you a bit more room in the budget for a really great subwoofer like the , which is easily my favorite sub for under $500. In truth, you have to spend around $550 before you can get a sub that can really dig all the way down to 20Hz and stay clean, tight and accurate while doing so. But for $320, all the STF-2 is really "missing" are the lowest of the low notes. What makes it such a great value and such a great subwoofer is that it is accurate, tight and clean, so it really enhances both music and movies. It's not just one-note rumble or a bunch of distorted noise. It's controlled, accurate, clean bass, and it's a MASSIVE step above any of the subwoofers that come in a HTiB package. More than anything, getting this sub will make the little bit higher price of the system SO worth while. The sub is what will make it FEEL like you're at the movies. Trust me, don't skimp on the sub. You really cannot get anything less expensive than the STF-2 that even comes close
Now you just need to power it all! You've spent about $650 for 5 speakers and a sub if you go with these recommendations, so you can certainly work with the remaining $350 to get a decent receiver.
Your best deals are going to be in getting a factory refurbished unit from accessories4less.com. They are the manufacturer's authorized online retailer for factory refurbished units. So you still get a warranty and the guarantee of the manufacturer that these are fully functional and "like new" units. Many of them are literally brand new and merely on "clearance" for being a year old and replaced by newer models. So this is the best way to get a new receiver at a great discount directly from the manufacturers, IMO.
Onkyo and Denon both offer some really nice receivers within your budget via accessories4less. The could certainly do the trick and easily leave enough room in the budget to cover any shipping costs on the other products. The is also a heck of a nice unit that will just squeek under your budget cap
So you'd be getting a better receiver than a HTiB, better Front Left, Center, and Right speakers, surround speakers that are about on par, and a WAY better subwoofer! And all for within your $1000 budget cap. I can't imagine there's much to complain about with that
Hope that helps!