Take a close look at what the software package is doing. If it is evaluating the tank using current standards, there may be a big difference between what was required then and what is currently required.
The vacuum design on tanks is pretty approximate. For example, the ASME code is more conservative than normally used for non-code tanks. If you're using an ASME procedure to evaluate the tank, you're probably overly conserative on the vacuum. The current (4th) addendum of API-650 actually has a vacuum design method in it, but I'm not sure how it compares with other methods. In the past, codes didn't necessarily combine wind loads and pressure, and that tank may not have been designed for vacuum and wind combined, if indeed designed for any specific vacuum.
I haven't dealt with Protectoseal extensively, but if you haven't actually asked, it might be worth a call to see if they have lower vacuum settings than what their literature shows. Or they might direct you to a different style of valve.
As far as substituting SS for CS, it wouldn't normally be done like that, but that's not as bad an idea as you make it sound like. The allowables in API-620 are fairly low, and SS stresses are usually high compared to yield, so there's probably not a big mismatch in stress. There's some variation in Young's modulus, seems like, and that would have some effect on the wind stability. Anchor design wouldn't be much different with SS or CS.