Looks like the repair tech and service manager can't find the problem or are to lazy to find the problem and they are trying to pass the buck on you by saying you are using a aftermarket part and the aftermarket part is causing the problem. Of course they will hand you a bill and your warranty will not cover the cost of the work. Pure dealer BS DON'T let them get away with it.
There is 2 reasons there is a lot of oil in the air filter
1- too much oil in the engine, the manual calls for 4 qts but you should only put in 3 1/2 qts when doing a oil change. Any excess oil will exit the engine at higher rpm through the crankcase breather and into the air filter and in most cases you will have oil dripping on the cam cover.
2- if the oil level is good than the crankcase breathers may be faulty which usually a bad umbrella valve in the crankcase breather.
I would take a close look at the lifters causing the top end noise.
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08 FLTR candy red sunglo,with 2015 103 HO, V&H Dresser Duals with Monster Rounds, Power Vision tuner, Willy Shiny Wheels and Forks and a bunch of other stuff.