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Help me out here. What is the advantage of that vs. the stock rubber part?

I agree. What advantage is there by replacing the factory plastic "air filter to throtle body" tube.

And I see the black PVC tube coming out of the lower air filter housing is used for cold air ducting, but it is probably in a bad place for water to enter the intake tract. The factory ones mount behind the headlight. I have also seen some mount where yours is, but suck air 90* from straight on. Both of these will help avoid water being splashed into the intake.

'87 4runner 37x12.50x15 MTRs
SAS, 4.88's, rear+front e-lockers
4x4Him --- Christian 'wheelin
4x4Him National Forum