Specification-wise they're virtually identical. Most notably, the B series has double the record length and comes with a newer computer (still running W2k though). There may be extra Java applications and trigger options supported as well, I'm not too familiar with those. It's basically the same thing.
Internally it's an update of the older design and is technically a different product. Although the improvements are incremental, parts and software from one generation are not interchangeable with the other.
Because the instrument was built as an integrated system, altering the qualified configuration is risky. You may trip up on hacks and bugs that laid dormant or were deemed not worth fixing, like the PCI error or some more insidious crash that happens 0.001% of the time. Proceed at your own risk.