Wow,  Sounds like we've got a very similar situation, and I totally hear your concern.  My husband and I - just came to the realization last night, as we sat watching the flock... that things have finally, & completely calmed down & the extreme chasing/pecking is over.  Our peeps are a tad over 13 weeks now...  and it seemed like it took forEVERRRRR... but the integration process you're doing, sounds great... just keep going!   
Establishing designated areas in the run, 'safe harbors' where they could get away from the hens is a good idea. I often found them all in there lounging, & put food & water in there for them too.  It was easy to do...  I purchased a few panels of 'no-dig, metal fence sections', at Lowes, and created a sort of barrier wall.  I anchored them down with the stakes, but raised the sections up off the ground, & supported it with bricks - which created a good sized gap that the peeps could scoot under, but it was too low for the large hens to fit through!  I also zip-tied plastic poultry mesh - at the top (it is hard and stands up well) which made the barrier wall a bit higher.  So a few of these spaces, set up in the run - give the peeps places to escape to, where they can relax - away from chasing, & the hens sharp beaks.
Here's the link:  
https://www.lowes.com/pd/no-dig-act...lwFpXx9aB7Ui484rqxkrNwTISRfM3bQkaAvrlEALw_wcB
Several friends here at BYC advised too, that when the little ones are closer in size to the big girls -it's much better, and I've found that this is true.  They can defend themselves better... but I just wanted everyone outside & to be happy, with peace & harmony in the coop!  But that wasn't to be, right away... it took a while... and a lot of time & attention, like you're doing!  Just keep going!!! It sounds like you're on the right track!   It's good you have 6 littles.  They'll be their own little gang. Even at 13+ weeks, mine still stick together... and stay away from the big hens, who, at this point aren't all that much bigger anymore. 
As far your question - how much is too much, or when does it become unsafe... trust your  instinct.  You will know in your gut when it's too much.  You don't ever want blood drawn... or feathers being brutally ripped out.  I knew - when I saw my  "Attila the Hen" going past the point of what I felt was the natural, pecking order.  She was unmercifully chasing, bullying, pecking and tearing out the peep's feathers... and they were all huddled in the corner, terrified of her.   I really didn't want to do it, I put the pinless peepers on "Attila"  - and they stayed on her for about a week... and that changed her behavior - sure and fast.  Here's the link:  
https://www.amazon.com/dp/B076CLT1BC/?tag=backy-20
 She could totally eat, drink, lay eggs, roost, and do all her regular stuff... she just couldn't chase the peeps. 
I hope this helped... Good luck 
@MYon,  and keep us updated!