Stratix 1 easy migration path

I'd let Quartus do the hard work for you (as ak6dn also suggested). Cyclone V should be a good fit and should alleviate some (possibly all) power rail capacity concerns - it should certainly be lower power. I think you should be able to use the same set of rails.

Throw your whole design at Quartus. You may have to specifically address any IP that the design uses, although Cyclone V will cope with a number of Stratix IP blocks. Once you have something that goes through the tools target a device with a similar package to your original part, then start assigning I/O to approximately the right area of the part, if not the same pin (if available) of the original part.

Whilst this will be a very iterative process, and potentially tedious, I think you'll end up with a pretty good match, hopefully with minimal board changes.

Cheers,

Alex