I think you're in the wrong forum (the is the second gen or post 2006 GV) - I also think that you've taken on quite a challenge - you would probably have been better off starting with a J20 out of a Vitara or a Tracker complete with the transmission of your choice.
As I understand it - the 2.0 flywheel (at least the 2.0 Vitara flywheel) will not fit under the 1.6 SideKick bellhousing and will require a custom machined 1.6 flywheel to be fitted to the 2.0 - I've included a link below with some possibly helpful information - I also believe the 1.6 transmission & transfer case is a fair bit shorter than the 2.5 auto unit - so some drive shaft work is likely to be required - bear in mind though - drive shafts are relatively easy in the general scheme of things you're going to be faced with - possibly motor and transmission mounts, swapping out the pedal box to add the clutch pedal and hydraulics, cooling, intake & exhaust manifolds, power steering pumps etc.
Even if the parts are available, it's going to be pricey.
http://members.cox.net/aftermarket4x4/2litertracker.htmlYou can also expect to have to do a fair bit of wiring - I hope you got the Aerio loom as well as the ECU - and you MAY find that the Aerio ECU lacks certain "controls" required by the GV - as an example - certain years & models of the GV have the 4WD controller as a separate "black box", others have it integrated into the ECU.
Last but not least - you MAY need to consider changing the final drive ratios.
Good luck.