Pop a cat carrier in the bathroom with a blanket inside, he'll quickly make this his bed and you can scoop him up easily when it's vet time and move him around the house when you need to.
Ask the vet if they can help with the fees for neutering as he's a stray.
Defo get the Zylkene going, it's worked wonders here on my bunch.
My Chubby ia an FIV +ve feral who took two years to learn to trust me, but he's now a proper little cuddlebum. His thread is on here.
http://www.purrsinourhearts.co.uk/index.php/topic,36495.40.htmlOnce he'd been neutered we kept him in the bathroom with an open carrier as his bed for two weeks, then he was allowed outside (he had already mastered the cat flap so could come and go as he pleased) and he did come back for his dinner that first day he was allowed out. He took up his permanent position under our bed and only showed downstairs for meals, when he would skulk about under the table and ran like hell whenever I made a move towards him, but he quickly learned where his meals were coming from so always came back indoors.
Eventually he learned to stop running away and I found his weakness for Dreamies, and his liking for being combed on top of his head. After that it was just a matter of time before he would let me groom his back, then chest and finally his tail end.
He's still worried about people moving around and still prefers to feed under the table, but is happy to be cuddled, groomed and picked up in the bedroom where he feels safe.
I hope you manage to get this little man sorted out - it sounds like he's already adopted you so it's not cruel to keep him penned up for a few short weeks when he will have a wonderful life with you afterwards.
It may also help him to have the TV on when he's alone in the house to get used to a background noise.
By the way, he'll smell much better once he's neutered too
As for weeing everywhere, Chubby hates cat litter so I used ripped up newspapers in his litter tray instead. It's messy but gets them used to using a tray.
I will say I was helped more by the folk on this site than anywhere else, so do get your friend to join Purrs too.