'99 R6 - Need help asap!

[Wicked1]

Hello everyone, I just registered a few mins ago, but im in desperate need of help. I bought a modded '99 R6 on the 19th last month (bad idea!) The first problem with the bike was the battery. It died on me while driving to my house from Miami on the Interstate! No biggie, just changed the battery. then about 2 weeks ago, my throttle cable snapped on me (i was parked :P)
just got that replaced yesterday. When I went to go pick it up from my friends house (he replaced the cable) I tried starting my bike, but the attery was discharged (battery was less than 2 weeks old!) so we just jump started it, and it ran good. but when I moved the throttle it didnt want to go over 6k rpm's then it slowly dropped down, then died. My friend noticed that the choke cable was disconnected, and said that my bike was flooding with gas because, maybe when the cable disconnected that it left the choke thingy open. So today I took off the air box and everything, searched for about hrs trying to find where the damn choke cable connects to. I recently found it (thanks to these forums) so I reconnected everything then tried to start her up. for some reason it takes a long time of holding the start button and alot of gas to even have her close to starting, it eventually started, but didnt go over 1k rpms (It sounded deeper than normal too). Then it just shut off, I saw a small amount of smoke escape through the batery area(oh, i just got a new battery today aswell) so I waited and decided to jumpstart my bke with my car, instead of kiling my 3rd battery lol. I hooked it up, than I went to push the button, and nothing happened. I can here the low click that comes from the battery area, but nothing else. I really need to know how I can fix this POS lol