You may well have read this as you seem to be doing much of what it suggests.

Cat Rescue and Adoption - Sheffield - Wizz Catz

I recently bought two adult cats (2 and 3 years) which I had to introduce to the semi feral that has adopted us.

I couldn't do the separate room thing, but I did do the scent transfer by stroking each in turn. There was a lot of hissing and growling, including paw swiping with and without claws, and chasing.

3 months down the road things are sort of settled. Each has a good idea where they belong in the pecking order.

The paw swiping, growling and hissing I think upsets us more than it does the cats. I would do the cat basket thing so that each can get a look at the opposition.