After playing since the new launch one of the things that annoys me the most is trying to automate this agricraft mod. Magical crops was essentially perfect on its own, but now agricraft adds in a twist to the crops and you have to put sticks down and what not. Then, if weeds crop up you have to deal with them. My suggestion, remove this unnecessary mod, and remove plant damage from magical crops. Even without the growth pulsers we can grow crops fairly quickly using automated watering cans. Agricraft is just redundant, and adds to the lag.
It works, I automated it within my first hour of playing. Use the Harvester block. The weeds are only an issue if you leave open cropsticks.