That sounds like a plan Trolle. I kept the original R65 metal pipes joining hoses to calipers too.
That was after I bought RS lower metal brake pipes  expecting they would fit nicely, just like you. I was surprised to find they were too long Â

.  Yet they look just the same length in photos  :-?  :-?
Are your stainless hoses the right length then?
Are you routing your brake hoses as I did (check my earlier pics on here). Â
I changed my R65 brake hose brackets (on the fork legs/ sliders) for R100RS brackets. So that, pipes and hoses were supported at the correct angle which BMW intended for hose coming from the RS fairing. I believe it is safe to bend the metal pipes, to fit correctly with these brackets. Protect them very carefully with rags or plastic during bending, avoid kinks or bending close to the ends.
Is the top hose the correct length and it's connection to the master cylinder at the correct angle so it will clear the top yoke, if not it may be cheaper just to get a custom made hose. If you're fitting a banjo conversion to the end of the upper hose, it is a 10mm banjo with a 10mm x 1mm thread for R series BMW. But I didn't see one on Earls' website.
Earls performance
http://www.earls.co.uk/ are an excellent company, though so it's worth asking.