These are my values for 0.5 yrs per turn, and it works to suit my taste. It will be very hard to have decent populations growth rates in castles later on, and when you use high tax rates in cities, they will grow very slowly as well. Note that governors will have a very low bonus to population growth with these values too (max +1%) and Squalor and Pest affect population decrease much more than before. Just try these values, tweak them a bit for yourself and you should be ready to go.
The problem with the farming level you mentoin is pretty weird, and I don't understand what could have gone wrong (in my changes, they are lowered for every settlement).
Code:
<factor name="SPF_FARMING_LEVEL">
<pip_modifier value="0.5"/>
</factor>
<factor name="SPF_FARMS_BUILT">
<pip_modifier value="1.0"/>
<castle_modifier value="0.75"/>
<city_modifier value="1.0"/>
<pip_min value="0"/>
<pip_max value="25"/>
</factor>
<factor name="SPF_HEALTH">
<pip_modifier value="1.0"/>
<pip_min value="0"/>
<pip_max value="25"/>
</factor>
<factor name="SPF_BUILDINGS">
<pip_modifier value="1.0"/>
</factor>
<factor name="SPF_TAX_RATE_BONUS">
<pip_modifier value="0.80"/>
</factor>
<factor name="SPF_BUILDINGS_FUN">
<pip_modifier value="0.5"/>
<pip_min value="0"/>
<pip_max value="25"/>
</factor>
<factor name="SPF_GOVERNORS_INFLUENCE">
<pip_modifier value="0.5"/>
<pip_min value="0"/>
<pip_max value="2"/>
</factor>
<factor name="SPF_TRADE">
<pip_modifier value="0.2"/>
<castle_modifier value="0.75"/>
<city_modifier value="1.0"/>
<pip_min value="0"/>
<pip_max value="25"/>
</factor>
<factor name="SPF_SQUALOUR">
<pip_modifier value="1.0"/>
<pip_min value="0"/>
<pip_max value="32"/>
</factor>
<factor name="SPF_PLAGUE">
<pip_modifier value="1.0"/>
<pip_max value="32"/>
</factor>
<factor name="SPF_TAX_RATE_PENALTY">
<pip_modifier value="1.5"/>