As for choosing where to reform, its not quite so simple as that. You must start at the centre (slightly south-east of where the Hai start from I think?) From there you can do either east or west or both. but you have to do east 1 before you can do east 2 and east 3 and so on. Likewise you must do west 1 before west 2 and so on.

So you can choose to do half your empire as persian and the rest as greek but you can't just do isolated chunks. If you can picture it, the reforms must be continuous and spreading out from the centre, start point.