If you put pods on there you will need more jet, however the trade off is more power. Do you still have the stock exhaust on there? It might be worth it if you're going to pods to get an aftermarket mid-pipe and end can. THe dan moto ones are the cheapest and if you get a Bandit 1200 model I'm sure it will work. As far as drilling slides, etc, etc. That is usually only required for some Dynojet kits. DO NOT GET A DYNOJET KIT!!!!! They have serious problems with the 2nd Gen Bandit. I know you're a GS1200SS but It's basically a Bandit with slightly different carbs and different bodywork. THis is what I would do if you're going to PODS.
Before ripping ANYTHING out of there, especially the airbox.
1. Pull the carbs right out of the bike
2. Make sure you're mixture screws are unplugged. If they are plugged with the EPA brass plugs(if you even have them) you won't be able to access them even with a $1000 tool. You must drill the EPA plugs so that you can access the screws. I didn't bother using a tool to adjust them I just use a flathead screwdriver bit, but you got the fancy tool so you're good.
3. Once you make sure that the plugs are drilled. Then set the screws according to the clymer guide.(I'll try and find out what the jetting is for you on that bike)
4. For now set them to the stock turns out.
5. Pull the floatbowls and read off what your 1. pilots are, 2. mains are so you know if you are stock or not and write down the numbers and post it here.
6. Check to see if the needle is adjustable or not.
For example on my bike:
I have 15 pilots 3.75 turns out from LIGHTLY seated.
and 112.5 Mains(100 is stock) for a stage 1. Yours will be different but they will probably be in the same sort of area.
Here is a pic of my carbs(different than yours)but they will all sort of look the same with the floatbowl cover off:
As you can see in the pic the mixture screws are closest to the engine and the plugs are still in there. A good way to get them out(If you even have them) is CAREFULLY drill the hole slightly larger so you can fit a self tapping screw in there and pull the plug out with pliers. Put some tape a 1/4 inch from the tip of the drill bit so you know you aren't drilling to deeply and phucking up the mixure screws. I think you use Keihen carbs not Mikuni is that correct? The main jet should be screwed into the emulsion tube and the pilot should be much smaller but near the emulsion tube. Unscrew carefully and look at the numbers on the side of the jets. THe "mid-jet"(????) is the starter enricher jet, ignore it if you even have the enricher circuit setup like mine.
If your having problems getting the airbox on there, loosen the boots on the engine side as well. That will give you more wiggle room to fit the box and the intake boots in there then tighten when everything fits. If you tighten the intake boots before putting the airbox in there so they are rock hard you need to be Arnold Swarzenegger to fit the airbox on there.
Do you have a Japanese import bike with the 180Km/h top speed limiter(you can get rid of that too).
As far as mixture screw turns out you can count in what you have now or just start around 2.5-3 turns from LIGHTLY seated. Don't go jihad tightening the mixture screws or you screw up the tips.
EDIT: Unfortunatly, since its mostly a Japanese only model it's hell to get any info on this bike. I can't even get pilot and mainjet numbers. But in general--->If you want to keep the airbox stock and just put an aftermarket mid-pipe and end can, One or two mainjet sizes up and a needle adjust or shim will probably be pretty close. With pods you may have to go like 20 sizes up and a larger pilot. If you can tell us what is in there now we can give you an idea of where you need to go. Even just taking off one of the outside floatbowls off, which can be done without pulling the carbs will at least give you an idea of whats in there.
Just to give you an example on my bike which has Mikuni carbs which has jet steps in 2.5
Stock with no aftermarket exhaust 100 mainjet
Stock airbox with exhaust 102.5 or 105 mainjet
Stage 1 with extra 1.5 hole in airbox lid and exhaust 110 or 112.5 mainjet <-----I'm here
Stage 2 with pods and exhaust 147.5 or 150 mainjet
While your carbs are different and the jet size will be different this gives you an idea of what kind of stepping to expect when jetting up. Since you have smaller carbs on there the stepping may be smaller. My Mikuni's have an artificially small pilot jet to get past emissions so you compensate with a slightly larger mainjet than normal. GET THOSE JET NUMBERS!