Why did Karl's new body revert to his former crippled self?

I believe you're on the right track when you mention the fight with the janitor. Around the time that Hans and Dr. Stein have the conversation about Otto (the chimpanzee) eating flesh after the brain swap, Stein says that it's because his brain was damaged shortly after the procedure; Karl escapes shortly after and is subjected to several blows to the head in his scuffle with the janitor, so I think we're supposed to take it that the damage to his brain -- sensitive in the immediate aftermath of the surgery -- caused both his murderous behavior and the paralysis to the right side of his body. Stein also makes a couple of other comments (I forget at exactly which points) about how it's very important that Karl not be subjected to undue stress and be monitored closely in the immediate aftermath of the procedure, too.

I don't understand this either.

Yes, the chimp became carnivorous after receiving the brain of the orangutan,
although orangs are NOT carnivorous by nature: "Fruit makes up 65–90% of
the orangutan's diet, and those with sugary or fatty pulp are favored ... Fruit
is the most important component of an orangutan's diet; however, the apes will
also eat vegetation, bark, honey, insects and even bird eggs." So, bird eggs are
the closest they ever come to carnivorism. The main point is: carnivorism is a
BEHAVIOR.

Karl, on the other hand, exhibited the actual physical manifestations of his previous
'deformities'; his physical structure actually changed form. Now, I can see how the
blow to his head / brain could cause changes in behavior - disorientation, violent
actions and killing the girl - but how could it possibly alter his physical structure??
Okay, I can see partial paralysis, like when one has a stroke. But his 'hump' grew
back??? I mean, it's not like he was just hunched over - you could see the growth.

I thought it was interesting and extra-creepy that it happened, but I wanted more
of an explanation, at least some sort of 'theory', or philosophical observation, to
be voiced by Dr. Frankenstein.

Yes, yes, I know it's a fictional movie, and I loved it (I love all the Hammer films)
but still ... I felt a little cheated when no one elaborated on that, since it seemed
(to me) to be an important issue, regarding Frankenstein's experimentations and
their success (or lack thereof).

*sigh* I'm splitting hairs, ain't I. 