Let's see if I can help you out. To start off with, you didn't say anything about checking and/or replacing any blown fuses. If you haven't done that already, that is the first thing you need to do. Remember, you will probably have fuses and/or relays under the hood too. Next thing is, that wire that you were working with that shorted out to begin with, did you take care of that already, if not, you at least need to make it so it won't short out again.
What we do know is that you have replaced the battery and the alternator although you may have damaged the new battery by completely discharging it. The next step you need to take is to charge the new battery on a slow charge which should be no more than a 5 amp charge. Preferrably a 2 amp charge. You need to do this to fully recharge the battery and do it slowly because it is less harmful to the battery. In almost every case of charging any battery ever made "the slower you charge a battery, the better".
It would be better to use a modern charger as it will control the rate of charge, stop charging when done, and inform you when it is done. Older chargers don't do any of that, but it's ok as long as you don't leave a battery connected to a charger for too long after it's done charging (like 24hrs too long).
It seems you may still have something that is drawing power from your battery while it is sitting so you need to check and see if that is the case. To do so, you will need a DC amp meter that will read up to 10 amps. If you have a DC amp meter, it will probably go to 10 amps. Disconnect your positive cable from the battery (+), put one lead on the positive post on the battery and one lead to the positive battery cable. With the key off and nothing else turned on, the meter should indicate zero amps or very close to that on the display. I would say if you get more than .100 amps then you may have a problem. If your meter reads over 1 amp, you definitely have a problem. If this is the case, the quickest way to track it down is to start removing fuses one at a time. Pull one fuse and see if the meter reading goes down. If it DOESN'T, put that fuse back so you don't lose track of where it went. If the meter reading DOES go down, your problem is in that circuit somewhere. After that, you're on your own till you give us more info.
The reason I said earlier that you may have damaged the battery is no battery likes to be discharged deeply (deep enough to not start your car is a very deep discharge for any battery of that type) especially a starting battery. Most starting batteries can handle one or two deep discharges without too much trouble, but after three or four times it's a crap shoot at best.
Hope this helps.....
