Body mounts: Not sure what you are using but I used hockey pucks on mine in 1995, no issues for 11 years then she got parked. It was my dd and off road beast.
the regular cab fj45 has no room behind the seats, looks like you built the same thing give or take and inch or two. Great work so far but why not make more of an extra cab or space for a passenger ?
Best to create a jig like apparatus to keep things square then tack weld all pieces. For frame section I would put 4 tacks on the C channel then weld top flat section of C then do the bottom of other side then when area is cool to touch weld the bottom of C section of first side welded then do...