WH, If everything else is correct as you say it is, my vote is for root bound. That's a lot of damn roots. Why don't you just put it in a 5 gallon bucket instead of 3 for the remainder? I disagree about a certain time to put plants into flower mode. It can be anytime. You could veg for several years if your container was big enough. What bad issues have you had with perlite? I didn't know it could cause any issue other than the need to water more often.