With my last orphaned litter I was having a difficult time getting them to poop. My male cat, LuckyDuck, finally stepped in and showed me how it was done:
He rolled them onto their backs and licked their tummys towards their genitals, sort of gently pressing his nose into their bellies. They pooped and when I tried it (with a washcloth over my hand) it worked!
To get them to pee, I would put a washcloth over my hand/fingers and while the kitten was upright (on tummy or legs) I'd use my fingers and 'massage' their tummy and privates. They would usually wet the washcloth for me. Don't try to hold them in the air for this, they need to be down on the ground similar to when their mother helps them.
I was not 'extremely gentle' or 'careful' of them, I sort of did it quickly and firmly. Mamma cats sort of knock their kittens around a bit. Maybe you are being to gentle and it isn't stimulating the kitten enough?