Why does Fuminori see his own body as normal? The only thing I can think of is that his body sense overrides whatever is affecting his perception of the rest of the world.
Perhaps it's denial? He sees himself as a monster (which would give another reason explaining why he's so full of self loathing) but he pretends that he sees himself normal to not freak Saya out. That or his condition doesn't affect how he sees himself, for whatever reason.
I'd think that it is his sense of self. The whole thing is mental, afterall.
Or maybe he got so used to seeing everything reversed that he had started seeing himself as a monster, and thus appearing human-like to his own eyes.
Considering he's sexually attracted to a little girl, and how in all the routes but the one with the least amount of bloodshed and suffering (ie, he chooses to become normal again, which is pretty clearly presented a Non Standard Game Over and not a true ending) he's generally cool with killing what he knows are innocent people and eating the flesh of children, I'd say he was a monster and therefore able to see himself normally.
Because he would go insane almost instantly and we would not have story, duh.
It can be argued he was already insane and we had this story because of it.
At one point, Fuminori explains that his senses were fine until he recovered his eyes. His brain then altered his other senses as a form of adaptation to what his eyes were seeing. It is never told directly but one could reason that some of his senses such as "proprioception" (the ability of knowing your own body and its position) didn't adapt due to being stronger than his sense of sight.
Proprioception, unlike his other senses which were affected, is largely subconcious.His visceroception probably wasn't affected either.
What's puzzling is how the tentacled Eldritch Abomination Saya is able to overpower other humans, but was helpless when she was raped by an insane Yousuke.
Anytime she attacked a human, she had 2 advantages, surprise, and the fact that they were looking at a whatever she was. With Yusuke she had neither of those.
Why didn't Fuminori attack Kouji while he was distracted by Yoh? He was firing the gun for a while after it went click, then hitting her for a long time afterward, yet Fuminori only came in after Kouji wasn't too scared or loud to notice him. If Yoh was still "alive" after he killed Kouji, Ryouko might have mistaken Yoh for Saya and wasted her chance.
Perhaps at that point in time, Fuminori was at his most sadistic and insane. Given the way he mentions how Yoh just met her demise, he might want an even bigger psychological edge over Kouji, and that would seemingly come perfect in the guise of, "That thing you just killed was Yoh, you monster." Approaching him while he was still engaged with Yoh might've triggered a flight response from him either way, and if he ran and had time to recover, Fuminori wouldn't have been able to finish him off. He wanted to root Kouji to the battlefield, lessen the risk of him fleeing due to Yoh's involvement, but at the same time be broken enough to not be at full fighting capacity while giving Fuminori, the weaker of the two, the biggest psychological advantage, perhaps even an emotional one given that Kouji just killed the only other girl he now saw as normal and part of his family, which Fuminori could use as emotional drive to propel his adrenaline and lust for Kouji's blood. Not that it works out completely, but given the state of mind Fuminori was at the time, it might've seemed the most logical thing to do. After all, if Kouji saw Yoh and then, knowing he was about to be engaged by Fuminori while this THING was boring a hole into his sanity, ran off, he might get anyone else involved in a matter of minutes, which put Fuminori and Saya at risk of being discovered, which was what Fuminori had as about equal priority to killing Kouji. Without Yoh being in a safe, human form and proven to be alive and unharmed, Kouji could have easily made things impossibly harder for the new Sakisaka family. Also remember that, while Fuminori isn't exactly sane, he still views the world as a disgusting horror and, if far enough away so as not to be at risk from being detected by Kouji before Kouji could be engaged by Yoh, he has to gather his nerves and navigate to the room they're in. At this point in the novel, the story doesn't play up how affected Fuminori is by the fact that he still senses himself as alive in his own little wretched world, but I think it's a safe assumption that, while his will to live and try to enjoy life has improved since the beginning of the story, he is still living in a world that he's had issues dealing with trying to both navigate and not be nauseous just existing in.