I did an 89 CSX Seca about 6 years ago with the 4AGZE. I got the front cut so I installed the larger front brakes, but left the rears as std drum setup.
Initially i contacted the approvals section and was told I would need to get a "full drive by cycle emmisions test" which was about $3500 from Orbital engines. Obviously I was disappointed but I wanted it legal so I spoke to an importer friend and I was put in contact with an engineer (PM me for name) who took care of it. He even had a huge argument wih the head of the modifications approvals section who adamently refused to pass it due to the emissions being untested. My engineer went over his head to the next level resulting in the fellow being told that the japs have better emissions than us so sign it. He wasn't a popular customer over there after that.
I can't remember the brakes being an issue since I was away and my wife met with him for the test.
For my next project (Cressida with 1JZGTE) the front cut disks were damaged so initially it run with the standard brakes (BA rotors came later). Before the engineer saw it the front disks were already warped, so i knew I had to make a change, but I just got them skimmed prior to the test (I wanted it legal before other changes were made). All they do is require 1 or two consecutive brake tests and if it stops in the required distance then you are fine. Based on this you should be fine and you might be best to not mention the changed rears and let them assume theey are standard.
Once the engineer gets his money (few hundred dollars) you get a peice of paper and can go straight to the pits for the normal inspection.
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