I think Mona was taking "friendly suggestions" from Alison by now, if not well before now.
Re: Jackie, that's a huge hint that Ali knew a lot more about Ezra than she's admitted to yet. They haven't really said what all Ali/Ezra talked about, but given that he was supposedly still in love with Jackie when he met Aria (is that even true?), it's not crazy to think Ezra spilled his guts about Jackie, including her plagarism, and Alison used that. (Remember, this Alison is big with dollhouses and moving people around like puppets; she's basically said so, at least in flashbacks. I think she's probably too stupid to look for skeletons in some random girl's research, though Mona might have caught it, IDK. But it seems likely that Ezra knew all about it since he was filming them all at this time, probably. I wondered if Ezra gave Aria the job to get Jackie off his back, lol).
We also don't know the real Alison/Mona story yet, but we know Alison was back in town by then (visiting Hanna in the hospital had happened), so I imagine Alison was at least "a helper" to Mona. We just haven't had but one reliable Mona/Ali flashback, from Mona, and who knows how reliable that was? (I think it was reliable, where she saw Ali in the Viv Darkbloom outfit, but there may have been a lot more going on. Like, if twins, Hidden Twin could have sent new-friend-Mona in to look for Alison; Alison was clearly hiding and "looking" for A, and didn't suspect Mona at all as her "A". —Or maybe Alison spilled her A fear to Mona just out of desperation. Regardless, we just don't know much about Mona/Ali's early days.)
I think the best link for the Hanna/Kate stuff is that Kate rides horses, as does Mona, and now we know Jessica/Bethany/Ali also rode horses: probable best link. Any of those "A" people could have blackmailed Kate to spike Hanna's drink and make her make a fool of herself. The doll tortured Hanna and kept her isolated, so I tend to think Mona blackmailed Kate, but maybe Alison helped with that idea. (Alison's scarier than Mona; I can see Alison doing it, too).
And like Mona later warned (S5), Alison's goal in picking them was to blame them. For what? "For everything." So after this episode, they'll have "prior charges" against them, even though they'd get off with community service. That makes me think Alison was playing Mona (if not ordering her around) in this timeframe.
I think it took Alison to think all the truly dangerous stuff on (like messing with Toby's car, and later Caleb's mom's car), while Mona focused more on the harassing part (sending threatening texts to to that doctor; getting Hanna away from the Liars; all still bad, but not "psycho" bad.) Mona clearly lost the reigns in their "game" some time in S2. But this is probably how she got it all done: Ali help.