If you like post some pics here of the plugs so we can all have a look. Like I said I'm not sure if you would want to adjust the jetting now it's up to you. However lowering the needles a notch is a simple job and easily reversable. Did the gentleman you buy it from give you an idea on what mainjet you have kicking around in there?
Actually hold on I may be mis-interpreting what the previous owner was doing did you say he put stage 1 jets(the receipt) in the stage 2 pods? If so then it will be lean even with the bad mid-pipe. It sounds like he was getting bad advice or something. If true, then my guess is probably he did the stage 1 and with the wonky mid-pipe it was still too rich. So he probably said to himself "Well I guess it needs more air" then went off the deep end and put pods on there when the real culprit was the mid-pipe. I believe even on the GEN1 bike the jets would be around 125 or something but I'm not sure with the GEN1. My stage 1 for my GEN2 came with the following:
25 .5 mm shims for the needles
3 sets of mainjets 107.5's, 110's, 112.5's(stock is 100)
1 set of pilots 17.5's(stock is 15's)
instructions on how to mod the airbox.
Well don't fret it too much at least he did all the hard work for you. All you need now is to get a proper mid-pipe and some proper jets which is like $8. With a stage 2 and mid-pipe and slip on the mains should be running in the 150 range. I'm running the suggested 110 mains and the 17.5 pilots with a K&N filter right now. The suggested setup for my bike is to use the stock filter but I foolishly popped in the larger pilots based on the instructions instead of my own good common sense and it was horridly rich at cruise and idle. Popping in the K&N temporarily solved somewhat but it's still too rich at cruise. Up top it's a little weak so I've ordered larger mainjets and the stock pilots that I'll pop in there in the spring. I still have the airbox on there with an extra 1.5" hole. So if I'm a lean up top with the airbox on there still you'd be really lean with pods using a similar mainjet. Which may explain the hesitation.
Here is a good site that sort of gives you an idea of what you should be running. You sound to me you know what the hell your doing unlike the previous owner so I'm sure you'll get her running right in no time. Check this out:
http://www.portablepct.com/fastlarry/banditfaq.htmI would just hold off to save you time and heartache until the real culprit the horrid stock mid-pipe is fixed that way your not jetting twice, however popping off one of the outer float bowls and having a peek is only about 15 mins of work that would definitely give you what the hell the guy was running. These bikes are almost ludicrously easy to get tuned so I wouldn't fret it too much. Every one and their mom on this site has a GEN1 stage 2 so you should be able to glean some good information. With the previous owner not remembering what the hell is in there is a little disconcerting. Who knows what he did, maybe he was trying to jet around the problem(shit stock mid-pipe) and now the jetting is wonky.
For example on my bike if I want to jet around the horridly rich cruise I can turn my mixture screws in so that the bike barely idles but cruise if fine and there is more power there but thats not a solution obviously. It's possible he decided that it was too rich and is artificially compensating with the needle or pilots instead of just fixing the problem. The stage 1 and 2 kits really only work properly with an aftermarket mid-pipe and slip on. You could jet it properly manually but then don't buy the kit, just a selection of mainjets. But maybe he read something on the internet and only got it half right like the broken telephone game where you pass a message along then see whats left of the message. He had the right idea but just didn't execute it correctly.