Much remains to be seen at this point, but it seems likely that Shoha damage is comparable or better than Fudo damage, assuming you make both hits on Shoha.
There's a few other factors in-play here though. The aftermath effect from Fudo is one. And I may be overstating it, but I'd like to see the damage from two-step self-chaining Kasha >> Shoha (Light) >> Fudo (Light again) using Sekkanoki, Sengikori, Meditate, and Hakagure before proclaiming "lolMasamune".
It bugs me (sorry, pet peeve) when SAM's discuss damage output without accounting for Renkei damage. If you wanna be a melee wrecking-ball, be a WAR or a MNK. If you wanna be a good SAM, you can't play it like a WAR; you gotta have tactics.
But I digress. Yes, given Shoha's reported hefty TP-based damage modifier and reported innate attack boost, having a Magian Trial "TP Bonus" R/Ex Great Katana (a la Hagun) is probably an excellent option now, if you're leveling Tachi: Shoha 5/5 ... much to the chagrin of those of us who recently completed 85 Masamune ... *grumble*
If you were considering starting a Masamune now, I probably would reconsider, but for those of us who've already forged the Masamune, don't put it up on a high shelf in your Mog House just yet.