I'm 99% sure that the JZX100 is already a single setup.
Anyway the Chaser has already been discontinued in Japan as of this year. I think all 2JZ and 1JZ engines are being discontinued.. some already are such as the JZA80 Supra, Mark 2 I believe has also been discontinued. Yes these engines are being discontinued for emissions. No idea about production cost.
Yes if you buy an aftermarket turbo you should buy a new ECU. Its not really as simple as just changing a setting on the handset I think. With different turbos you probably need to upgrade different things. For example in a GTR if you edn up getting a single conversion it is usually a pretty big turbo. This means upgading a lot more things than just the turbo.... such as intercooler, ECU, injectors and the whole fuel system like fuel pump an regulators etc, AFM's lots of things..... in order for all these things to be tuned properly aftermarket ECU is needed.