From my experience the pump takes quite a few weeks to re-establish something like the previous erect penis size. At the beginning it was clear that a lot of the tissue had tightened up, and it didn't take much enlargement to feel quite uncomfortable. Added to that, because its size was small there was room for a testis to get drawn up as you report - even more uncomfortable!
Like Chris J I have the SomaErect pump from my local NHS. It came with an inner tube of smaller diameter, which I used at first. There was associated with that an inner rubber seal, and that was important in reducing the space for the testicle to get involved. I still had to manually hold my bits out of the way though.
Slowly but surely though the ability of my penis to enlarge increased, and the problem got forgotten. After a couple of months of regular pump use it was reassuringly similar to a "proper" erection, which indeed slowly then became possible. Now the insert tube of the pump seems too small to imagine I ever needed to use it.
Good luck, and have patience.
(Sorry, I can't add any personal advice on the leg problem).