It's not for the faint of heart, but what involving Cryptography and Certificates ever is? As with most arduous journeys its always a good idea to have a guide and for this one I highly recommend working with Dan Griffin on JW Secure. Dan used to be the developer for CryptoAPI 1 (what is now the legacy Crypto layer in Windows), as well as one of the smartcard and CryptoAPI NG (the new Crypto layer in Windows) developers.
You just can't go wrong with Dan at your side on a project like this, another useful resource is The Soft Pedal Shop; this is run by Doug Barlow another ex-Microsoft Developer who worked on a number of core security components including the legacy CryptoAPI framework.
What about other resources that might be of use to you on this trip? Well some that come to mind are:
As you can see there are lots of options for you, do you want to add new cryptographic algorithms to all versions of Windows? If so start looking at the legacy framework, it has short-comings but it exists everywhere. Are you targeting VISTA and Windows 2008? If so the new CryptoAPI NG addresses much of the short-comings of the legacy framework and should allow you to get going much faster too.
Is your project about integrating a smartcard with Windows? If so seriously look at the new Card Module (minidriver) model for integrating with CryptoAPI unlike the legacy model of Cryptographic Service Providers (CSP) you get to focus on your core competencies with this approach and not worry about all the other things a CSP needs to do.
Then there is the .NET framework, it offers a lot of great functionality like XMLEnc, XMLDsig, Extensible Cryptography and Certificate validation all available in all .NET languages. If your looking at doing work in this area I highly recommend picking up Brian Lamacchia's book on .NET framework security its a little dated now but still very valuable.
And one can't forget the COM support for XMLDsig in MSXML, its easy to use and available via all COM enabled languages.
In my time at Microsoft I have had a chance to contribute to all of these technologies so if you have questions feel free to ping me and I will do my best to answer any questions you may have.