You won't get hold of an car where the engine and the transmission ECU are separate. That situation only exists on the JDM Crown Majesta I believe, which are so rare it's untrue. I can only speak for the MKIV (which due to gearbox and VVTi has a unique ECU from previous marques) but a lot of the functions are separated out - ABS & TRC are a separate ECU, body electronics are a separate ECU, etc. Unlike the Toyotas of old the PCB in the ECU isn't silkscreened with a 3 letter code for each pin as there are simply too many of them in too high a density to be able to fit it in!!
I am part way through using a MKIV VVTi engine for a project, at the moment I am dismantling the stock loom and working out pinouts and stuff for the ECU. Fooling it into thinking the gearbox is still there and the selector lever is set in a specific gear seems the best way forward for mating a manual gearbox up.
Have a read of the forums on http://www.v-eight.com/
Edit: I believe a model of GS in the states also got the VVTi engine with the same (fake) 5 speed box as the MKIV, so it's worth trawling the US sites for workshop/wiring diagrams etc.
Edit 2: There are sump differences between the revisions of engine too, if a front sump application is alright for you then no worries, but you can change it to midsump by using a few parts from a Soarer 1UZ, sump, oil pan, baffle plate, oil pickup etc.