My guess is that the K&N filter and slip on without jetting is making an already superlean bike even leaner. The popping through the carbs is a sign of a lean condition. Do you have the mixture screw plugs drilled out? Turning them out a bit would help but you definatley will need to rejet or at the bare minimum put some shims under the needles for it to run well(still would be lean up top). You probably just lost some horsepower there. If you want to do it on the cheap (~10 bucks)try this:
You can drill the mixture screw plugs out(unless AUS bikes have them open) and turn them to 3.75 from lightly seated to start.
Put in 110 mains put the ORIGINAL filter in not the K&N.
ANd drill or cut a 1.5" hole in the top of the airbox cover.(The part you unscrew to change the filter) Keep the snorkle in
This gets you 90% of what a jet kit will give you and is a good starting point.
If you want to jet for a closed airbox and a K&N filter I would suggest starting around 105 at the minimum and at least a shim or two. Maybe 3.5 turns out?? The standard turns out on a stock bike according to the haynes manual is 3 turns from LIGHTLY seated(don't go crazy on those brass mixture screws) for Euro, Canadian and Australian bikes. THe poor US with their EPA just lists "Pre-set" :-)
If you want to do the bare minimum, popping in the stock filter, and setting the mixture screws out a bit and shimming the needles, until you have some jets will help alot. I've had a K&N filter and was trying to jet around it just for fun and with even with the extra 1.5" inch hole cut in half it was still a little lean on 110 mains, you're 4 steps leaner at 100 mains.
If it was my bike I would do this tommorrow: Pop the stock filter in temporarily, turn in the mixture screws untill they are lightly seated. Use a magic marker and a hand mirror so you can look underneath the carbs and make a line so that you can count the turns out precisely for each carb. I adjust the screws with a screwdriver bit and a cheap plastic dental mirror, it's tight but it works and its cheap. Count out 3 turns out for now so you are at the "stock" settings. It's going to be lean but be patient. Drive the bike until it fully warms up, at least 20 mins. Then turn the mixture screws out a 1/4 turn at a time untill the idle gets to the highest point before the idle starts going down again. For example you turn to 3.25 turns out, the bike idles higher, 3.5 turns out, higher still, 3.75 turns out, oppps idles less ok I'll settle at 3.5 turns out. Even though you will have more power at 3.75 turns out you are really just compensating for a lean main jet(or keep it there if you're happy with it for now). The correct setting would still be 3.5 turns out. Adjust the idle back to 1200 RPM. Another good test is when the bike is fully warmed up lightly blip the throttle if the RPM dips below set idle then recovers you are too rich on the pilot screws, turn in a 1/4 turn at a time. Alternatively if you lightly blip the throttle and the RPM hang for a bit then drop down you are too lean turn out the screws 1/4 turn at a time.
Even with the screws correctly set you will get some popping due to the PAIR emissions crap on the bike. Don't worry this is normal. Abnormally loud popping, or extreme amounts of popping will indicate a lean condition. For example my bike pops just a little but its more of a grumble and light little pops or burbling, if I turn the mixture screws in half a turn the popping gets a lot louder, cruise isn't as stable, etc. Every bike is different but my guess is with the stock filter in there and the slip on pip you have you'll probably end up around 3.25 or 3.5 turns out. You will still need to at least shim the needles. I got some from Dale but if there is a radio shack or a hobby store near you you can buy them. Depending on the thickness, I would put 1 or 2 shims on there as they will probably be thicker than Holeshots.
What shimming entails is putting shims underneath the needle seats to raise the needle(make midrange richer). I'm not sure if your bike has adjustable needles or not the Euro's do, Canada doesn't and the US doesn't. If you have a adjustable needles you lower the C-Clip a notch or two to richen up the midrange.
If you would like to have a quick look, and have a very small rachet set with screwdriver bits, you can take off number 4 carb cap without have to pull the tank off and lift the slide out of the carb and take a look at the needle. If the needle has a c-clip and indentations on the needle you can adjust it, if not you have to shim it.
BEFORE YOU TAKE OFF THE CARB TOP: WARNING
There is a little dinky o-ring at the front of the carb, under the carb cap, which gets lost very very easily. I highly recommend putting a rag or something up against the front of the carb to catch this if it falls off. Take the carb cap off CAREFULLY.
THis is what I have for reference:
17.5 pilots(stock is 15)
110 Mains (Little lean up top will go to 112.5's)
4 turns out on the mixture screws(may change with larger mains)
5 shims on the needles. (may change with larger mains)
Holeshot 5 degree advancer
I'm under 3000 ft altitude so I need it to be a little richer than most guys and I think my raggedly-ass hole I cut is a little larger than 1.5 inches and my Muzzy is a little more free flowing than the Holeshot can(2" vs 1.75").
I bought a jet kit from Holeshot which is great because Dale gives you tech support.
It's worth the $120 bucks in my opinion the bike just screams now.
If I find my jet kit as I need the 112.5 mains out of it, I could send you the 107.5's but its probably easier to call your local shop. Here are the part numbers for your pilots and Mains:
Mikuni Jets
Pilot: VM28/486 - 15's(stock)
Mains: N100-604 - 100(stock)
The second number after the first is the size they come in steps of 2.5. So my setup as I have 17.5 pilots(smooths cruise alot) and 110 mains would look like this:
Mikuni Jets
Pilot: VM28/486 - 17.5
Mains: N100-604 - 110
Addendum: Even with the pilot screws correctly set when the bike is fully warmed it may sneeze a bit when dead cold. THis is normal when the bike is cold. If you adjust the pilot screws to "cure" the sneeze when it's cold it's going to be super rich when warmed up. Do not attempt to adjust anything on the carbs until the bike is fully warm, at least 15-20 minutes of riding.
Also what octane grade is 98? If that's premium your just wasting money. The Air/Oil bandit series doesn't have enough compression to warrant premium gasoline. You should use the lowest octane available without pre-ignition or pinging. Using "Premium" is just wasting money on these bikes. I even have a 5 degree advancer on mine and while I can run well on 87 or regular when it is super hot out I get a slight bit or pre-ignition so I use 89 or mid-grade and get zero pinging and it runs great. Using premium for an engine that's not built for it could theoretically lose power and have more coke deposits from an incomplete burn. Premium gas doesn't mean you get more horsepower. Octane is an ignition inhibitor not a power rating.