When the bike was sold new, it had the correct jet for the engine with standard exhaust, silencer and air filter, It may now have an after market (Not Yamaha) expansion pipe and silencer, you are also talking of a different filter. These things are changing the bike from how it was, the danger is in running too lean, too lean can cause overheating, in extreme cases ahole in the piston crown or possible seized engine. This is why you need to jet when you start changing these items, although i must add that I doubt you need to make big changes, thats why I said go for the next two sizes up from standard
BTW Markyboy27 is looking into jetting on his 125 Dragstar, have a look at his recent posts, you will learn a bit from them
See plug chop