Hi Lizzie,
I agree, having RC ancestors in London is incredibly difficult and frustrating - been there, done that!
Just two crumbs which may or may not help you. I was amazingly lucky in that I emailed several RC churches about mine (yes, they all still have their records) and the one that answered was the church they attended! St James Spanish Place. They were incredibly kind and helpful to me - whether they took pity because I was in Oz, I don't know. But they looked up their records and found mine for me.
It may be in the wrong part of London for your man, but might be worth getting in touch with them just to check.
Also, do you know about parishregister.com? A great little mob who are are putting online the baptism registers of all East London parishes, plus a lot of watermen and lightermen stuff, plus other things. They have made CDs of various Roman Catholic registers of parishes in London, which are available for purchase. Have a look at their website, see what you think! If you like, you can arrange to get their monthly e-newsletter.
Hope some of that helps.
MarieC