In my opinion, the comparison should be between the Stage Customs and the Pearl Exports. In any case, the Stage Customs are generally considered the better kit, both from the woods used and the finish (lacquer vs. wrapped). Like the other posters said, try them both to see which sounds best to you, both from behind the kit and in front of the kit. Both kits will benefit from better heads than stock - I've found that two ply heads like the Evans G2 sound good on less expensive toms. I own a Stage Custom kit with coated G2s and tuned medium, it sounds very nice.
Yeah, I would be comparing Exports to stage customs. The Export kits are also laquered nowadays. I'm partial to the Pearls because that's what I play.... I would prefer a Tama Rockstar Custom though.
I had the same question, only comparing Customs to Pacific LXs. It is good to point out that you should follow your ear. But if I had the choice between Pearl Exports and Stage Customs, I would go with Yamaha.