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Starting issues. new alternator & battery. junction box??

My husband and I have an 87 TV 2WD, and this is the 4th 80's TV "Lightship" we've owned. We bought this one in 2012 and it just started giving us problems within the last 6 months.
Here's the gist:
Van won't start, intermittently, since last summer. Battery terminals are clean and cables are tight. Took the battery in and it tested good (was new last August), but it showed that the alternator was putting out a little less than normal (it was the original factory alternator). Had the alternator replaced last week and it started and drove fine for a few days.
Today, we took it out for a few errands around town, and at the second stop, it died. Starter was clicking, but it wasn't turning over (in other instances, it was completely dead.. no click, nothing). We got a jump and drove it home. In most instances, when we jump it, it starts right up immediately... except for when it was dead in our driveway a few weeks ago (and the temp was very low out.. in the teens), and it had to be charged for 10-15 min before it would start.
I read something on the Toyota Van People forum a while back about a corroded junction box (behind the battery?) being the cause of a similar issue, and it was fixed with a wire brush and some vaseline. I have no idea what this is or how to locate it (and the young guy we had replace the alternator said he couldn't find the junction box, but the fuse box seemed fine. I think he might be younger than our van).

One other possible factor is an after-market alarm system that was installed by the previous owner. It's a Viper and has updated our 80's Lightship with *futuristic* automatic locks, an alarm and a remote starter (very amusing to hear the van go "bwoop-beep"). 
I love this alarm system because these vans are notoriously easy to steal. My husband had 2 stolen, and I once unlocked & re-locked a stranger's TV with my key to turn the headlights off in a parking lot so it wouldn't have a dead battery (gotta look out for each other!).
After the alternator replacement last week, the remote starter would start the van, but then it would shut off after about a minute, and it would keep trying to re-start, die, re-start, etc. We hadn't been using the alarm for a while, thinking that perhaps it was causing a drain on the battery, but started using it again after the alternator replacement.. then it died.

So... questions:
Could it be a corroded junction box? How do I find this to determine if it is?
Could it be the alarm system draining the battery somehow? Where the heck do I take it to have that looked at?
Any other suggestions?
We're newly relocated to N. Colorado and these vans aren't as well-known in this area, so haven't found a solid mechanic yet. Most mechanics I've called don't understand what they are, don't know where the engine is, and don't even have the Chillton manual for anything older than 1990. We found this really nice kid who's really reasonable (he replaced the alternator), but it'd be helpful to have some pointers for him.
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