Your best bet would be to read the wiki.
Yes, I have read the wiki, but didnt clearly understand)
1. How to get correct XDF for my engine and ECU?
2. Should I edit just ESKONF? or CDHSH etc too?
That definition is for a early aph beetle and isnt even close to your file.
3. Looks like APH and my AVH is very similar engines. My car is old too - 2000 year. Are you sure that definitions should be different?