I don't think these cars are quite as picky about batteries as some European cars or other more high tech stuff. Probably the easiest thing would just be to pop the truck and charge the battery directly if you can. That would take most of the variables out with the alarm system. Even if it was armed, I have a feeling as soon as you start charging it you would likely be able to disarm it with your keyfob or the key itself if it started going off. That being said, if you charge it from the trunk you wouldn't even have to worry about that I don't think.
And that's not to say that a dead battery can't or won't cause strange issues that can be hard to track down, more just that I don't think the Viper is as sensitive in the sense that I don't think things need a lot of resetting or calibrating or anything like that. You could probably jump it and the alternator should keep it going, but if the battery is way dead that's generally just not very good on the system as the alternator might be trying to push max charge through things. If it's that far gone it might be easier to just buy a new battery for it and start fresh, but I'd think if it was regularly driven before being parked for 2 months that it wouldn't be too bad and you could probably even jump it fine. I know I've done that on mine when it had enough juice to turn the engine over some, but not enough to start it.