just as a quick fix for timing besides getting and using a timing light is bring piston 1 up to tdc and then set the head at tdc install timing belt and start it up. but best and most effective way is use timing light and go from there
a6 with the y series cam gear and you will be good to go. the y series gear correct the timing issue caused by changing the cam or you can get a adj cam gear and be done
if its a vtec head you cant use a non vtec vc unless its from a y7 or the obd2 d15b non vtec. vtec vc have spark plugs facing foward and non vtec facing back(exlcuding ones mentioned and maybe others)
and on a side note the ex has a a6 motor but the tranny is not like the si trans. its a shorter final than the dx but not as short as the si final. ill edit when i get the exact difference in the ratios
IIRC cali smog rules say that the motor must be of the same year or newer with proper smog legal stuff like cat and obd ecu. so if you go obd1 convo and use proper ecu for the car you should be ok but i dont live in cali and dont have smog so someone else can chime in and give you a better answer
a signal is sent from the ecu to the vtec solenoid. go on youtube and search for how vtec works and watch the video on there to understand more about it
with the si trans you can use your stock axles and hub but you gotta keep the axles and hubs from the chassis. all the d-series inner parts are the same but the outter parts are different. so the si tranny will work fine with the stock axles and hubs, i know this from experience.
the 5th gen axles are diff lengths than your 4th gen ones. there is NO benefit of having a hydro trans in your car. find a ex/si trans or a dx 5speed and have it done correctly