I use stock needles and shim them. Jet according to what the engine wants not a specific size. I am not now and never was a believer in using a suggested jet size for any engine. Taking the time to jet to the engines specific needs is where the most is gained. I know of all the folks who tried jetting to someone's recommended jetting only one was able to attain the same results without adding a timing advancer to the mix, but then again their total gain wasn't as solid across the board as jetting to the engines needs. Defined as driveability with no flat spots and a smooth power delivery right from idle to redline. I hate flat spots! I also use the stock foam filter nothing more noting less.
The question has been asked many times before unfortunately I have been reluctant to let the info I have gained out and for some cutting into the airbox is a little frightening. Remember what I said about creating a vector. Because you need to apply that both to the airflow while sitting still just as much as when the bike is doing 100 miles per hour. Going too big on your secondary openings or putting them in the wrong place will be detrimental to that smooth power from bottom to top and you must also remember that if you get caught in the rain or have to wash the bike you can let too much water inside and have a blown engine in no time flat. Talk to the Harley riders you will find that Air intake mods are responsible for lots of engines getting blown during heavy rain when they travel to those distant meets and get caught in the rain without notice. Around home when bar hopping they just don't go out when its going to rain or sit it out till it stops. Its actually funny to watch when a group of 7 or more ride in together and one or two have to stay behind and wait out the rain because they have a big water scoop attached to their air cleaner.
Please remember that all my gains have been measured with the airbox mods, new plugs a valve adjustment and the rejet as well as a good carb sync I never honestly tested it with just the rejet and air box mods or with a 100 % stock exhaust. I have tested with everything from drilled stock pipes, slip on (both F1's and suppertraps) and D&D 4 into 1 headers. and all put the bike between 100 and 105 HP respectively at the wheel.