It is not allot of work to move the TB location on an upper. Most anyone with aluminum welding experience can get that done.
Any of the uppers will have smaller runners than what came on the 3.5 DOHC, swapping to these may not be the wrong thing. I do not have any other Montero uppers other than the original on my SR so I do not have first hand answers for you. Maybe it is time I go back to buying parts and learning more.
If anyone has any later 3.5 or 3.8 upper intakes not being used I would be very willing to develop something that may get this group a more efficient work around for the DOHC intake issues.