Ignition For Modified Engine

I am having an EJ207 bored and stroked for my rebuild. Apart from this, everything else is stock. I know the safe thing to do is retard the timing a couple of degree before I go WOT during logging, but I have a question for general direction of the timing tuning. Should the properly TUNED timing map be less than the stock map?

You won't know until you tune it. Changing the bore/stroke can change everything about how the combustion occurs. That's why you have to measure the torque (with a dyno), and tune the ignition timing to maximize it.

Yes I understand this quite well from the course and what you are trying to say, but a dyno and a protune are not possible in my country. Since I had to rebuild the engine due to a broken valve, I put a larger piston and bigger crankshaft. So I'm venturing out into this activity on my own and I am looking for an answer how a tuned map should be for overall. I am getting a knock monitor for the road tuning as well.

As David said, you're going to have to find out what your specific engine and components works best at*. One may expect less ignition timing to be required, but that's not always the case.

*for example, you say everything else is 'stock', in which case one may expect the boost level to be a little lower and charge temp's also to be lower, which may allow a little more timing for MBT.

If you can't get to a dyno, then just use the existing stock / OEM timing. It's the best guess possible.