Hi,
Apologies for the late response - and hopefully I can help. Our situation is a little different because my wife came to Germany under different rules 12 years ago so the process now is quite difference. After legally living and working here for long enough she obtained a permanent residency permit. We're in the state of Hessen in Germany, although the rules are common across the whole country.
So I can't give much real experience about applying for a new residency card now (although if you have specific questions I can read German and will happily help!). That said, my wife transitioned recently from the old style visa vignette to the new residency card and that took around 6-7 weeks from making the application to receiving the card. I imagine that's a typical processing time for either existing or new applications. Our experience of applying for such things in Germany (i.e. visit visa application for her Mum to visit) is that it's quite different to the UK process. They ask for a specific list of documents and you must provide those, accurately, nothing more, nothing less. It is then much more procedural - they check for inconsistencies (I assume) and then issue the visa/residency permit. It's more formal bureaucracy and less of "making your case" to an entry officer as in the UK. Be prepared for paperwork and the devil really is in the details - make sure everything is consistent. That's a pain but at least if you provide all they ask you to then it should be smoother and less anxious than a UK application.
As for needing an EEA Family Permit to travel from Germany to the UK (after setting up here) - I read that it is quite possible to take the Calais route without one (just passports and marriage certificate) and get a 1A stamp. We've applied for the family permit because we want to travel by plane and have heard they can be difficult at the airport.
For registration at the Einwohnermeldeamt - that is something I know and have experienced! To answer your questions:
a) Is the application form free?
Depends on the registration office but usually there's a small administration fee (a few euros - not much).
b) The registration process is pretty much instant. You arrive with the relevant docs (passport and proof of address - like rental contract), fill out the form (or fill it out beforehand), wait in line (usually it's just turn up - no appointments - go early!), submit it to the counter, pay the fee (if necessary) and then they print out the completed document and give it to you there and then.
c) As above
You get the certificate straight away.
There's a short but good guide in English to the registration here:
http://www.toytowngermany.com/wiki/Resi ... gistration. As the link says - this registration is the first thing you do - before applying for any residency permit etc. (they'll want to see that you've done it). It's also important to do it quickly (1 day - 2 weeks, depending on the state) after arriving. There's an example form someone translated into English here:
http://bit.ly/16EO2C0 but I'd recommend to go along with someone who speaks German!
I hope that provides a little more information - I'm sorry we have no recent experience of applying for a new residency card. Definitely happy to help though if you have any more questions!