I'd like to make some suggestions as far as POPs are concerned. I know not so much about programming, but I know a lot about game mechanics, so I hope I'm helpful:
POPs and Culture/Religion:
1. I think you should key each province to their starting religion and create a religious minority in that province if the religion changed since the beginning of EU2. Thusly, if Venice converts Crete to catholicism in EU2, the converter tool would see that Crete's original religion was orthodox, and would designate perhaps 5% of the region as orthodox and 95% as catholic. The exact numbers would have to be tweaked.
2. A cultural minority should probably be created in the following circumstances:
a. A country's home provinces should only have cultural minorities created in the event of that country gaining additional cultures during the game. For example, if Byzantium stays catholic, it should get italian cultural minorities in some of its home provinces, probably at random.
b. Colonial provinces should probably all have a small cultural minority keyed to their specific location. Aztecs/Mayans in Mexico, AmerIndians in America, etc. This should be keyed to the specific province.
c. One or more slave pops should be created in every major area where slavery was legal at the time of Vicky's startup. This should be in addition to the normal pops, as EU2 doesn't even consider slaves and doesn't factor them into city population. I would also argue that indentured farmers, serfs, and the like should be factored in and counted as slave pops as well.
POPs and militancy/consciousness/plurality:
1. Consciousness should be directly tied to your country's innovativeness slider (probably where the center of the slider=about 4 consciousness, and each notch up or down puts it up or down one, with negatives being 0), and plurality should probably be tied to centralization (although I'm not quite sure how plurality works yet). Militancy should probably be tied to the actual revoltrisks of each of your provinces, where 1%=1 militancy or so.
POPs and type distribution:
1. Okay, here's where things start getting tricky, but here we go:
a. Aristocrats/Capitalists: Keyed to the aristocracy/plutocracy slider and to the mercantilism/free trade slider. The tool should check for EU2 COTs and place Aristocrats/Capitalists in and around them before placing them in other provinces.
b. Clergymen/Clerks: Keyed directly to the narrowmindedness/innovativeness slider. The tool should check for the EU2 provinces with the highest population and place clergymen/clerks in and around these provinces before placing them elsewhere. +1 Clerk in any province which has every civic building upgraded.
c. Soldiers/Officers: Keyed directly to the quantity/quality slider. This would have to be the most lopsided as far as proportion goes; in order to have as many soldiers as officers you'd have to be way way over on the quality side.
d. Craftsmen/Farmers&Laborers: Keyed directly to the Free Subjects/Serfdom slider, although no province should start with a craftsman but no factory.
Other Ideas Concerning Policy Sliders:
1. Having more plutocracy should increase the number of clippers you start with, while having more aristocracy should increase the number of cavalry divisions in the reserve pool.
2. Having more innovativeness should increase starting literacy, where maximum innovativeness should probably be about 50% literate.
3. Perhaps more defensive doctrine should mean more existing forces become allocated to the reserve pool by the tool.
4. More naval should probably increase the number of clippers you start with, and perhaps more land should increase the number of divisions in the reserve pool somewhat.
Oh well, that's everything that popped (no pun intended) into my head when I saw this project. Good luck on it.
EDIT: Oh, and any province which is occupied by a country that does not have its culture should get a cultural minority POP of the primary culture of that country. That's all for now!