If you have the old Tamiya kit--I wouldn't worry too much about it. It still builds up to a very nice model. Judging from the CAD, there are only a few minute differences that would really be a deal breaker--if you cared enough.
1. Veryfire's model (may) correct the scaling of the 16" main battery. Probably the largest issue on the Tamiya kit.
2. Bulkhead detail! But the Pontos set already takes care of that (from your complaints, you've already bought it).
3. Splinter shield thickness.
4. 20mm splinter shielding straddling #3 turret has corrected shape.
5. The short paravane (skeg?) at the bow. Could be scratched if you were so inclined.
6. Adding the captain's hoods onto the last 2 remaining 5" gunhouses (strangely omitted from Pontos set, but shouldn't be hard to dig up spares somewhere).
7. Veryfire's Missouri has some shell plating, but it appears incorrect anyway. But at least it's there, if that is your sort of thing.
8. Possible bow shape correction on the Veryfire kit??
9. Possible seaway addition to superstructure 03 level??
10. Properly hollowed out windows surrounding bridge and conning tower??
11. Both models have incorrect struts/gussets for 20mm splinter shields. CAD and old Tamiya model represents these as raised rectangles, whereas on the actual ship, they were rather distinct triangular shapes (Flyhawk's 1/350 ultimate detail set offers corrections for these, or you could scratch them).
If those issues aren't too big of a deal (or beyond your means to correct), then the old Tamiya model may actually save you the trouble of sanding off the bulkhead detail anyway! In my experience, they tend to be overscale. I wouldn't disparage the Pontos set or the old Tamiya classic. Veryfire just has the benefit of being the new kid on the block.
But with a little bit of effort, both should build to be respectable models of the Mighty Mo (or any of her sisters).
On a more related note;
Mr. Kim, if we purchased the basic set, but decided to upgrade to advanced set at a later date, is it possible to purchase an add-on set (like those offered in the earlier 1/350 Yamato releases)? Thanks.