Hey guys,
So I've been scouring the posts and reading the Clymer manual, but so far the solution/steps to check this out have eluded me.

As I stated in my "WTB various Parts" post, just got an 89 and turned out to be a bit more work than I initially thought.

Anywho...when buying the bike, the seller told me that the battery was dead b/c the bike had been sitting for a year so he used my truck to jump it and start it and it ran fine so I bought the sucker.  Took it home, went to Walmart, replaced the battery/charged it and then put it in the bike and the bike is still having problems starting.

The engine turns and turns but it never picks up to start.  However, if I attach one of those emergency jumper boxes to the battery, the bike starts up immediately like nothing is wrong.  But if I remove the box, the bike idle eventually slows further and further until it dies after about a minute or so.

Where should I begin looking? (the battery is new and charged and I charged the old battery and what do you know, that sonuva gun is working on a test lightbulb too!)

The bike came with some parts including the main wiring harness from a 1997 GS500E.  Everything is the same except for the fuse part of it and the fuse seems to have extra connections.  Should I even bother switching out the wiring harness or is the problem somewhere else?  If I do need to switch it out, what the heck do I do with the fuse portion.

Thanks in advance. 
"the mechanically not-so-inclined student"

I would start by stopping the assumption that the battery is servicable. Take it to a shop and get it load tested.

Typical Walmart and other batteries have the electrolyte drain tube on the wrong side for a GS500. When on the side stand, the battery can start to drain out that little tube because it is on the left side. On a GS500 you need a special battery with the drain tube on the right side so it doesn't drain out when bike is on the side stand. So check your electrolyte level. Maybe it has been drained out too much?

Usually the battery fluid level is so low it doesn't matter. The only time it matters is if the battery boiled over with it side standed, AKA, you sitting there revving it for hours on the side stand, and it has a bad R/R as in its sending AC to the battery. Those things all need to be the case, side stand+revving+1hr+bad R/R.
In 5 years with the WM battery, I've lost acid one time, when I crashed on the left side ... mind you I crashed on right side in 97 and the battery survived, in fact I squeezed 5 years from that battery till my 2001 crash on the left which killed it, cos a bunch of morons transported the bike in their tow rig with it lying down I believe. I ended up going to hospital with a broken shoulder.
Cool.
Buddha.

Thanks guys, I'll check to make sure none of that is happening and thanks for the heads up on the battery, I noticed that when I placed it inside so I was just going to drill a new hole on that side for the vent.

New developments:  I switched the petcock switch to prime and tried a few more times and now the bike starts up but idles high, doesn't really start when it is set to ON

1) I'm probably a moron and the problem is between the handlebars and the seat
2) The PO jerry-rigged the petcock up when he last "cleaned" the carbs (I'm going to check 'em tomorrow)
3) I check the wiring harness and it all seems fine.

I'll keep this updated, but I'm starting to think it isn't an electrical problem.  I still appreciate the quick replies though.  You guys are faster than bringing it to a mechanic!

Check your air cleaner too, if it's overdue for replacement/cleaning the bike will act just like you describe.  Mine did that in March 08 when I had about 30k miles on a stock air cleaner element, close to 60k on the 02 bike.  Would crank and crank without even trying to start so thinking it was flooded I closed the choke jets and cranked the starter and it immediately tried to start but wouldn't keep running without the choke.  I finally caught on to the problem and put in the new air filter element I was waiting for spring to install and it started right up and was fine after that.  Dirty filter will restrict air flow causing the engine to suck more gas thru the enricher circuits.

Guess what?  Now 3 years and almost another 30k miles later it's doing the same thing again.  Had to put the jumper on it yesterday and again today to get started.  Starts immediately with the jumper unit on it really spinning the engine. Already have a new air filter on the way so will just jump it as required until it arrives I guess. Restarts all day after jumped in the morning.

I changed the air filter at 30k and 60k miles on my old 97 GS and put 80k miles on it without ever having that problem but it had the old 2 circuit carbs with stock jets and ran much leaner than the 02 does with the 3 circuit carbs.

And Buddha is right, after the oem battery was replaced with left drain batteries I never had a problem with any leaking battery acid with the bike parked on the sidestand.  I just dropped the drain hose down the left side and let it hang on the 97.  On the 02 I ran it across from the left drain batteries to the right side also without any leaking  problems.

thanks jack, i'll check the air filter when i clean the carbs and remove the tank tomorrow