I've just gotten my pfx file built, using Jane's "SetupBuilder Code-Signing". It was invaluable! I explored the latest Windows SDK (Windows 7 and .NET 3.5 SP1) and found pvk2pfx.exe and signtool.exe in \Setup\WinSDKTools\cab2.cab. Did not find capicomm.dll anywhere so I hope I don't need it.

By the way, all I had to do for the new code signing certificate was to supply the DUNS number and put my domain registration in my company's name instead of mine.