Well for the PAIR shit, block off plates if they go on to the front of the engine just below the exhaust headers then it will work fine. Then you can remove all that PAIR crap, it kill about 5 pounds of crap and tubing and makes valve adjustments way easier to get to. It also eliminates most of the de-acceleration popping when putting on and aftermarket exhaust and some claim it to help idle and down low smoothness due to better exhaust scavaging. All the PAIR shit does is add air to the exhaust gasses to fool the emissions people there is less emissions then there really is. I wouldn't bother with it just get rid of it. Be sure to cap off any open holes that are created like the airbox and the vacuum line, etc.
Do you want to permanently have an exhaust sensor installed on the bike? I'm not sure why you would want that but if you do you can either drill and tap a hole for the sensor after the collector box, either in the mid-pipe or near the end of the end can. Also if you're using the K&N filter without jetting for it, it will drive like shit. These bikes are already lean as hell out of the factory, with a K&N it's going to get even leaner. To make it function properly if the rest of the bike is stock you would need to go at least one up on the mainjets and adjust the mixture screws and probably add a shim or two to richen the needle. But if you're going to go to all that trouble you might as well just go to a stage 1 which will add 15 horsepower and drive alot better.
This is the best bang for your buck:(I have the next Gen so someone will have to check these jet numbers, going by Fast Larry's site)
Aftermarket end can with mid-pipe $150
127.5 Mainjets $12 type Mikuni N100/604
Radio shack shims for the needles part # 64-3022A $5
2" hole cut in the airbox lid, you can do it.
K&N filter, you already own it.
Mixture screws: 2.5 to 3 turns from lightly seated.
Horsepower gain 14-16 and a lot more grunt in the mid-range. Anything else to be honest is a waste of your time. Do not be tempted to pop on an aftermarket end can with mid-pipe without jetting or the K&N without jetting. You will actually LOSE power especially up top. Don't believe K&N's bullshit about just popping it on there and it's an instant 5 HP. The bike has to be jetted for any changes in throughput of air to the engine. Also do not buy an end can if also doesn't come with a mid-pipe. Since the mid-pipe is like %60 of the restriction of airflow on the bike some guys here have been saddled with an super expensive end can that does almost nothing because it didn't come with a mid-pipe.
If you're going to go to the trouble of popping off the carbs to drill the mixture screws you might as well wait until you can do a stage 1 at the same time. These bikes are stupidly easy to tune and you'll thank yourself later. This is a general guideline and should be confirmed by someone with a stage 1 on the Gen1 but this should get your close:
14.6mm float height(float height very important! make sure they are all set properly, mine were all over the place from the factory! Confirm with manual in downloads section)
2" additional hole in the airbox lid
2 radio shack shims on the needles
2.5 to 3 turns out on the mixture screws
K&N filter
Aftermarket end can with mid-pipe
Recommended you swap out the soft brass float bowl screws with stainless steel hex bolts, makes changing jets stupidly easy. I believe they are called "M4" 6mm bolts but don't quote me. Just go to Home depot with a screw and match them up. If the aftermarket end can and mid pipe doesn't come with a centre stand stop you can fabricate one for a few bucks out of sheet metal. Some guys JB weld or drill and tap a hole in the top of the centre stand and glue or screw in a little rubber bumper. All these solutions are cheap. I can tell you what mine is if you like for my Muzzy. You can also buy a kit if you're not comfortable will jetting and they will give you help, such as Holeshot.
Here are some links to get you started:
Cheap exhaust and mid-pipe people are raving about out there:
http://www.dan-moto.com/DM_US/gsf-bandit-600-1200-n-s-wholesale-18_20_58.htmlDoesn't come with a centre stand stop but if you have $3 in sheet metal you can make one like my Muzzy which attaches to the centre stand bolt. Or buy a fancy one for $30 at holeshot.
Holeshot stage 1 kit if you want the support:(pricey though your paying $150 for $12 in jets)
http://www.holeshot.com/bandit/bndt_b12_stage1mod.shtmlI know it's alot to take in but I would NOT install that K&N until it can be jetted. If you don't want to go to a full blown stage 1. Usually getting an aftermarket exhaust and using the stock filter with a jet or two up on the mainjets and a shim and a mixture screw adjustment will help you out alot. If you're going with the K&N as well you'd have to go up another 1 or 2, but at that point you might as well go to a stage 1. Since you're doing all the work for one why not have the extra 15 HP?
If you don't want to wait until you get all the parts you can get alot of improvement by drilling the mixture screws setting the float heights properly, setting the mixture screws the same(I think 2.5 or so) and if you want to try to pop in the K&N in there buy the radio shack shims and add 1 shim underneath the C-clip on the needles or the plastic spacer. That will get you pretty close though up top is still going to be pretty lean. Maybe do a poor mans carb sync as well:
http://forums.banditalley.net/index.php?topic=13207.0Good luck!