Essentially what you're doing is running the engine lean. NOT good for it at all. A simple filter swap isn't as bad as a whole new high-flow intake, but it's still not ideal if it really is a big upgrade in air intake. As far as running stock jetting w/ an aftermarket pipe/filter... don't do it, you're cheating yourself out of performance and hurting your bike. If you're gonna spend $300-750 on that setup, do yourself (and your bike) a favor and spend $30-75 and jet your bike properly. Otherwise, you're just wasting your money. Don't neglect your carbs.
No clue on 350 jetting numbers though, sorry.
Get on my level Brother