Oh the world of working mommas! talk about guilt! we hear you there sweetie, been through that road a number of times, with the consequent grannie and me having to play the nasty momma role...
In fact, i beleive your ds is quite the smartie pants. I would doubt though that the sleeping issues are manipulating related. More like a " i want my mommy" call, and who can blame him for that? being the smart cookie he is, he's realizing you're not around that often and on top of it, it was a coinciding time with his illness, so you'll have to work hard on rebuild that part of the "trust" that has broken. Don't you worry it sounds worse than it is. By being by his side and giving lots of extra cuddles this following weeks you'll get there.
I'm not specialized in Discipline issues, can only talk to you about what has worked for me. Maybe you'd like to post something in the Discipline forum where you'll get heaps of good hints and knowledge from the ladies there. But what has worked for us is to avoid the no's and turning them into yes, like with the plant i would go like: i know that is fun, but so is XX and offer and alternate activity where you make a big fuss about and he'll find he's pleasing you (hey, if he gets a smiley from nana he might as well expect that from you and since you come with the NO that would explain why he's angry and starts biting), so you might find the alternate choices world a lot more fun and less distressing than the world of no's.
Also, when he says something (or does something) that hurts you, try to breathe, leave and come back after counting to 10. My son is the same, the other day he was really a big bag of mischief and i was constantly limiting him so he told me: mommy go away yes? nina here (nina is his nanny) i wanted to smack him and cry my lungs out at the same time (i cried out at night with my dh, i was so sad he stopped loving me and wanted the nanny instead). Of course nanny doesn't mind to clean up after the mess he makes and will rather do so instead of disciplining him. But they get the idea, that maybe granny or nanny allow them to do X but mommy won't but is as funny as they are, don't you worry just don't take it personal. When he told me to leave i said, (instead of the smacking and crying i had already planned LOL) i know nina lets you do this but hey, I know the sheep song and she doesn't and started to sing a made up song. He followed me right away and forgot about his plans of firing me LOL.
Whenever ds is doing something dangerous or mischievous I say: i'm going to play here with my little people (draw, read a magazine, wahtever) cause Manolo won't play with me...oooh it's so funny, too bad he won't join me... he's right there in the blink of an eye. SOmetimes all they want (sp. the working mamma kids) is your attention. They won't loose it because of a tantrum or a mischief so if you don't give a bad connotation to it and pretend you don't care, they'll stop the bad behaviour cause they'll see they're not getting what they want (attention) and will look forward to do the things that will cause mommy to pay attention to them... don't know if i made some sense but that was pretty long winded for one who doesn't give discipline advice LOL...
As for trying wi/wo, i wouldn't think of it as a "leaving him to cry" method since you're returning every single time he's in a distressed crying. You go in, and REASSURE which is the most important part of it. It's not like he'll be on his own to figure things out. You'll just be there by his side, teaching him an independant way to do things. And you'll do it together. Yes, there might be tears, but remember los are reluctant to new ways and tears are their only way to express frustration, so you'll not be making him suffer... just teaching and sometimes it hurts to learn but when you look back, its totally worth it!
HTH and keep us posted!