Were both valve covers updated 01+?
 

On my 99, I've got my pass. side valve cover off and I got to thinking. Is the baffle design modified(improved) on the 01+ covers? If so, does anyone have a pic of the old vs. new design side by side? I don't have access to a 01 pass. valve cover, but maybe I could modify mine. Otherwise I'm thinking of going to a breather filter on that side. So, any opinions on that would be welcomed. Thanks.

What motor do you have?

If your motor has a PCV system, don't remove it. It is supposed to be there and you risk damaging your motor (due to excess pressure in the crank case).

Not sure what you mean? 99 3.8 motor. Yes it has PCV.
I'm referring to the poor design of the 99-00 driver's side valve cover. It would allow excess oil to get sucked up into the intake. They improved the design on 01-04 valve covers. I'm curious about the pass. side one, not sure if they updated that one as well?

On my girly's '98 3.8L the PCV valve is on the passenger side valve cover, which means that the blow-by gasses are sucked out of the motor from the passenger side valve cover and those gasses go into the intake. Filtered air is sucked into the drivers side valve cover due to the gasses getting sucked out of the passenger side. So I don't see how oil could get sucked out of the drivers side valve cover because air is being sucked into the drivers side valve cover. The air is moving in the wrong direction.

The reason I suggested not removing the PCV system is because you mentioned you wanted to put a breather filter on the drivers side valve cover. That would mean you are disconnecting part of the PCV system, effectively nullifying its benefits and potentially putting your motor at risk.

I'm pretty sure the valve covers remained the same from 94-04. Both 99-00 and 01-04 have a vacuum lines from the upper intake to the driver side valve cover as well as a line from the pass valve cover to the air intake tube. I wouldn't suggest using a breather however if you do want to prevent oil from being sucked into the intake you could add an oil catch can, which as the name implies catches oil being sucked in. Hope that helps.