Have you seen the two Dangerous Prototypes analyzers? The Logic Shrimp is 4 channel, 20MHz, 256K samples and the Logic Sniffer is 32 channels at 50MHz 6K samples or 16 channels at 100Mhz with 12K samples.
They use an open source analyzer project Sump Analyzer Client that you might be able to target with your project giving you a ready to run client.