The 2.3 engines are good and strong but the 2.0 litre especially the B207R version revs more freely. No issues with the manual gearbox but stick with the 5 speed version and not the old 4 speed as strength on a modified engine is suspect. There are 6 speed gear boxes available from the 2003 onwards Aero models BUT these are not really for fast pace but more for long distance cruising on motorways etc.
I am not aware of any of these engines being run on motorbike carbs. I am a turbo man through and through I'm afraid. The ECU is nothing to fear and gives you much greater scope with regards to tuning.
What sort of power are you looking for?
If you stick with the turbo then opt for the HPT rather than the LPT version. You will want a minimum of a TD04, Mitsubishi do a hybrid for this model with a larger exhaust impellor. The turbos are fussy with the quality of oil so skimp here at your peril.
A stage 1 remap from an Aero engine should see you about the 250BHP mark, 280BHP which is about stage 3 is the max really without at least changing the pistons to the forged versions at about £500 for the set (3" exhaust down pipe needed). After this you could go to stage 5 "315 BHP plus" which will also require a high pressure fuel pump i.e."Walbro 255L" and a 3.5 fuel pressure regulator, higher flow injectors.
Horse power in excess of these figures is huge huge money! and requires massive internal engine work.