wiring will probably cost you around $80, more or less depending on how much you shop around and what size wiring you get. I would say get at least 4 gauge wire so that you aren't limiting yourself immediately, and 2 gauge would be preferred.
I also ran my power wire down the driver's side, it doesn't matter which side you run the power down as long as you have the power wires & the signal wires seperated from each other so that you don't get interference. Don't forget to fuse the power wire.
I'd also say consider a factory HU. If your brother drives the car after you, worst case scenario you can tell him to give you some money if he wants you to leave your head unit in the car. Otherwise you can pull it out and put the stock one back in. By using a LOC, you're probably going to end up tapping into the rear speakers. That means that if you ever adjust the fader, you're going to lose bass because as you adjust the fader to the front, there's less power going to the rear speakers, and a weaker signal to your subs also. That gets annoying fast if you use your fader at all. Also you'll have to rely on your amp to adjust any crossover points. An aftermarket head unit gives you a dedicated subwoofer signal, that you can adjust independently of your other speakers (won't be affected by fader/balance, can set crossover, level output, etc). Also an aftermarket HU will put out more power to your other speakers making everything sound better, and nowadays you can get some pretty decent HU's for less than $150, and even have USB inputs for ipods or whatever else.
Baja subs, if you're getting them for practically nothing then you can't complain. They'll probably produce sound, lol. In all seriousness if it's your first "system" you'll probably be happy, and whatever aspects you're unhappy with about them you can just use as a learning experience, and build off of that so you'll have a better idea of what you want out of subs next time you're buying.
You can buy a prefab box but if you do I'd suggest buying some liquid nails or something similiar and running a bead along the inside of the box to properly seal it. Prefab boxes are notorious for air leaks. Personally I'd avoid prefabricated bandpass boxes like the plague, and really just stick with sealed if you're buying off a shelf.
For wiring, LOC, and a box, you should be able to keep it under $225 pretty easily. If you buy that stuff used off of craigslist or ebay, you might even be able to get everything for under $100.
edit: forgot to talk about amps. My opinion on amps is to buy the best amp you can afford to. I'd rather have too much power, and simply turn the gain down, than have a smaller amp than I'd like to have. Especially for someone new to audio, when people buy smaller amps they tend to try and compensate for that by turning the gain on the amp way up, or using the bass boost, both of which are horrible ideas and could lead to you blowing your subs from distortion or overheating your amp.
There are some good value brands out there. I'm not familiar with baja subs but I'd imagine they can take at least 200wrms a piece, so I would say buy an amp capable of at least 350watts rms, the higher the better. Brands that aren't amazing but pretty good for the money IMO would include HiFonics amps, Profile amps, and then if you buy used that opens up a whole world of Orion, MTX, RF, Alpine, etc. I would actually say to avoid Pioneer and Kenwood amps though based on personal experience.
I'm surprised none of these guys with audio experience haven't said this earlier... but... you're making a mistake with this set up 
I mean sure it will work, but your audio quality will be very poor and it won't be loud at all. You need to figure out exactly which subs you have to match up the output of the amp so that you don't overdrive it... and I doubt you want to underdrive it and not get your full potential. A new deck is critical for your audio system to sound great, it is the absolute most important part of your system. Realize that a new deck doesnt just give you a little more "tuning" ability for you sub, but actually gives you clearer sound, more punch on ALL of your speakers, and typically way more features, such as USB input. 
