While i'm not trying to be offensive, to me it looks like you took one of the most gorgeous fan-made ships, and ruined it.
As for the retexturing work itself, it looks pretty good... however I tend to agree with Dr McCoy1701A on the matter, in that section 31 ships (if they even exist) would likely be very close to their official Starfleet counterparts in terms of looks. Of course, Section 31 ships could be equipped with experimental technologies not known to Starfleet Command, thus allowing them to use experimental "phaser" or torpedo technologies, or stronger shields, or better engines etc. (without changing external appearance)
EDIT: For example
Give the ship dark purple "phasers" and dark purple "shield glow" to indicate temporal technologies, and give it a modified photon glow of some other color to simulate experimental torpedo technologies. That would be my suggestions rather than retexturing it.