The first step is to make sure your bike runs well with the stock setup. If you're starting with a poorly-running bike, you're not going to have much luck using this guide. Get the bike running correctly with the original carbs, airbox, filter, and jetting, and THEN worry about pod filters.
The second step is to inspect your filters, make sure there's not a big rubber lip on the inside that blocks the vacuum and air bleed ports on the intake side of the carbs. This will make the bike run like crap. For example:
Big problem with CV carbs and cheap pod filters. People think it's because CV carbs don't work with pods, and that's bupkis. CV carbs, especially '70s and '80s carbs without tuned resonance chambers (like the Honda V4s) respond quite nicely to pods or stacks, so long as the ports are not occluded. That's not to say '90s bikes won't benefit either. The 500 Ninja greatly benefits from pods!
Once that's taken care of and the carbs are clean, it's time to think jetting.
On a cold day, give it full choke and try to start the bike. Does it start easily and idle high with the choke on? After 5 or 10 seconds of running, can you give it gas and rev it a little? If it is difficult to cold start on a cold day, difficult to keep idling even with full choke, and/or has to idle and warm up for a long time before you can rev it without the bike stalling, then you need a larger slow jet. Go up one size, and see if it's better. If Keep going up until the bike cold-starts on a cold day with choke, idles high with the choke, and can be revved almost immediately -- BUT it is still difficult to cold start with the choke off. If it starts easily on a cold day, with a cold engine and no choke, then your slow jet is too big.
Once that's dialed in, hold the throttle open to about 7000 rpm, and listen. Do you hear a lot of crackling, snapping, backfiring, or just plain straining to rev? If so, you need a larger main. Keep increasing the main size until you no longer hear that. If you however hear a gurgling, especially on overrun, it's probably too rich. (This is almost likely not the case with your bike as it is set up now). This will get you in the ballpark. Once that's done, take it for a ride. Lots of full-throttle, hard acceleration runs. If it seems lean, richen it up. If it runs better, you made the right choice. You can try going up another. If it runs worse, go smaller instead. Eventually you'll find a jet where it starts to run badly on the lean side, and starts to run badly on the rich side, with a range of jets inbetween that seem to run all about the same. Choose the one in the center of that range.
Finally, the last thing to concern yourself with is needle height. Once the bike is running fine at idle and at wide open throttle, run it at a constant speed on the highway. If it surges or feels like the bike is changing speed ever so slightly, even though your hand isn't moving on the throttle, chances are it's lean, and you need to add shims under the needle (or if you have an adjustable needle, move the clip on the needle down one notch). You also may experience a lag when you crack the throttle open from crusing velocity. The bike may fall on its face for an instant, and then accelerate normally. This is also indicative of a needle that needs to be raised. The higher the needle, the more fuel you get at partial throttle. This is a very good indicator, because when you crack the throttle open quickly, the slide reacts to air pressure quickly, but the fuel takes a half second to be pulled up out of the carb and atomized by the airflow. If you're already running lean, adding more air makes it much leaner for a split second, and the bike will lurch before the fuel catches up and it starts accelerating.
If your needle is too high, your gas mileage will go to shit. If you have a stock needle without an adjustable clip, and you're running rich at partial throttle (and everything else is set up correctly), then you'll have to get aftermarket adjustable needles. However, it's almost always the case that stock needles are too lean and a shim or two is all it takes. (If your midrange is rich with pods and stock needles, chances are the problem is your jets are too rich, and you need to go back and try this whole thing all over again) Radio shack electronics washers (.020" thickness) are perfect shims. Just buy a package of mixed electronics washers for $7 or so and you'll have a lifetime supply.