I thought all sc300 and sc400 have the same body plugs but I don't know 100% for originally vvti cars 98+, non vvti I know they are the same body plugs and are the same as found on a soarer 1jz harness.
now the number of wires sticking out of them may be more on the 400, but they are the same plugs. usually the body plugs are unique to a given chassis, which is why a soarer harness normally plugs into a sc chassis when you extend it about a foot. a 1jz harness for a SC means it has body plugs for an SC, with me so far?
are you saying that the body plugs are different on the 99 sc400 vs your 95 sc400 cause that would be odd, I guess they could have been a vvti thing but I think they should be the same or similar. you should use the whole 99 motor and engine harness. the only thing you would need to do is sort out any wire difference on the body plugs themselves if they are the same, and add a few wires for the obd2 port IF you even want an obd2 port.
the 2jzge didn't really change from 92-97, it stayed non vvti, and there were only a couple changes on the main engine harness (2nd crank sensor on 96-97). when you change the engine harness though none of that matters it just matter that the new harness has the correct body plugs. being from a soarer and made to work for an SC already it should have the same body plugs and plug in to an SC chassis.
as I said earlier, for example on a supra turbo you can plug in the obd2 ecu on an obd1 harness and with no other changes it will run the motor properly. it only takes another wire and the existing wires from the obdd1 port to wire up an obd2 port. so when you say obd2 system, really its only another wire and a plug and the right ecu, so it has nothing to do with the dash and rest of the car u7nless you want to replace the whole dash harness vs adding 1 wire and a plug (would be a waste of time and totally unnecessary). maybe if you need some help with your v8 conversion then post a thread and I can try and help out where needed.
according to this thread it plugs right in