@ShiroxCloud It seems that the more complex a wiki is "under the hood", the worse it fared going over to UCP. FFWiki took the summer quarter to get out from under a number of bugs brought on by backend issues. They're mostly working as of this writing. As for my two, they didn't get too far down the customization rabbit hole and came through mostly unscathed. DQWiki's got a good group of folks keeping things on the square; and then Mana didn't need too much more than a solid face lift. Anyway, this whole thing is a marathon and not a sprint, so take whatever time you need to set things straight.
@Moviesign Think Star Trek, but with a twist. I believe they used a condensed font for box headers. They also have different color schemes for each game in the series.
Looks to me like their custom navigation boxes at the bottom of each page need a little bit of extra work since the migration. It seems that theme customizations were removed. The resultant theme looks very bland and does not mesh with what should be a sci-fi atmosphere. @ShiroxCloud this isn't anything on you and your team, but the changeover makes for a lot of other work needed to set right what is out of whack. Good luck.