What Ashrem said. Going negative culture and/or pop is really not that big of a deal, likely the biggest issue you will have with that is inability to do extra buildings and upgrades for events, but with recent changes it might be less of an issue. I usually prefer going negative pop rather than culture because then you can still do residence upgrades. Also, at least for Elves residence dimension changes are probably the least convenient in this chapter. But this also means that you will likely need to drop a ton of residences when upgrading, so may as well drop them ahead of time.
As far as upgrading the farms, it depends. Basically, the higher number of farms you can fit, the fewer upgrades you need (as it becomes counterproductive). IIRC with 70 farms I only upgraded them to L2, and never waited for mushrooms. If you're only putting up 10-15 farms then it will probably make sense to upgrade these to L3 or even L4. It will still take forever, but will be faster than un-upgraded.