I guess the most historically plausible way to do it by first taking 90% of the 1399 population from EU 3(if you want the converted save to take place in 1399), then modify the population based upon the province's tech level, the tech 4.0(or maybe 3.5, not sure what the average CK 2 tech level is by 1399), provinces lower then the base tech should get less then the 1399 EU 3 population, and vice versa, 40% population for each point they have extra in tech, or 40% if they have 1 tech level less.
Example: Holland in EU 3 has 10000 population(it actually has about 30000, but this is just a example), if Holland and Westfriesland have exactly tech level 4 in CK 2, it has 9000 in EU 3.
Then it should about be as follows:
Tech 3: 5400 ---- Tech 3.1: 5760 ---- Tech 3.2: 6120 ---- Tech 3.3: 6480 ---- Tech 3.4: 6840 ---- Tech 3.5: 7200 ---- Tech 3.6: 7560 ---- Tech 3.7: 7920 ---- Tech 3.8: 8280 ---- Tech 3.9: 8640 ---- Tech 4.0: 9000 ---- Tech 4.1: 9360 ---- Tech 4.2: 9720 ---- Tech 4.3: 10080 ---- Tech 4.4: 10440 ---- Tech 4.5: 10800 ---- Tech 4.6: 11160 ---- Tech 4.7: 11520 ---- Tech 4.8: 11880 ---- Tech 4.9: 12240 ---- Tech 5.0: 12600
I think it would make sense that the level of technology would affect the population size of the main province city, better technology would give better farming ways and more people might have left the agriculture for the city the more advanced a nation is. Also, the use of the original EU 3 population should be used to prevent things like a very populated Iceland(the Icelandic cities in EU 3 have just like 1000 population each, I dont want this to become absurdly higher).
I also think this way of providing population is very flawed but I just cant think of another better way now.
Have the province income determine the base tax and levy size the manpower(I haven't really figured out how to do determine that though). Then use the base tax and manpower to add back some of that 10% population that was initally being taken off.