One could argue that the whole film itself is a headscratcher. Almost nothing is explained about the nature of the Cool World, nor are we given much insight into how the world came to be. It just... is.
Was Holli insane before she turned into a noid? And if not, how did turning into a noid make her insane?
1: Yes. 2: The drastic physical and possibly emotional shifts just made her unstable- mentally unstable as well as physically unstable.
Also, in regard to Number 2, she had no experience with the emotions that came with being noid. When talking about "what the noid dames got", she says, "when they feel something, they really feel it. When they taste something, they really taste it." This suggests that doodles lack the emotional feelings that tie to physical experiences. When Holli became a noid, all she experiences from that point is new to her, and thus she suffers an emotional overload that causes that instability.
What was the point of trying to kill Professor Whiskers?
She was trying to threaten/bully Professor Whiskers into helping her. But she was acting recklessly (due to being temperamental and sociopathic) and semi-inadvertently stabbed him in the process.
Because Gabriel Byrne can't do a cartoon superhero voice? Shot in the dark. The other good question is why Superhero Jack barely looks like him?
Near the end of the movie, why did Holli start turning into a zany toon instead of returning to her normal form?
Holli wanted to stabilize her form, and simply fixated on the spike as the one thing with the power to do that. But as the Professor told her, nobody can control the spike
Why was Jack able to just return to his house and car after spending an untold number of years in prison? Did the state of Nevada just keep everything for him?
Presumably he was very well off financially and was able to maintain his payments and whatnot. Think about it, he walks into the comic store and several individuals recognize him almost immediately and in real life if you're not Stan Lee comic writers don't have a hard time flying low key.
Since Jack wouldn't have been able to make any money off the publication of Cool World, we can rule that out. In prison, one can't run buisness that generates income. Jack probably had to pay restitution to the victims's family as well as possible alimony. He probably lost most of what he owned (to his presumably ex-wife) due to this crime. It's possible he inherited the house owned by his parents (who probably passed away while he was incarcerated). It, along with the car, might be the only asset he has left. Jack had to politely turn down the fangirl (who invited him to hang out that night with her and her friends) who worked the comic book store explaining that he had to "get his feet back on the ground". She was dissapointed but sympathetic; immediately understanding what he meant.
What do doodles get out of sex, if they can't "feel" it? Holi Would complains to Frank Harris that she wants to be real, so she can really taste things, really feel things, and have sex with real men. This would imply that Doodle sex isn't that great. Yet it's desirable enough for Lonette to long for sex with Frank Harris. And at the end when Frank becomes a doodle, both parties are excited to finally have sex. What were they going to get out of it, without feeling anything?
For that matter, what did Lonette's customers at the restaurant get out of the food and drinks she served them, if they couldn't really taste any of it?
Holli envies that Noids can "really feel things". I think that doodles CAN feel things, but Noids feel them even more. Doodles can feel enough to want things and be happy or unhappy, Holli is just greedy for even more because that's the kind of person she is.
It's more likely that this is simply a "grass is greener" perception on Holli's part.
So in all the years that Frank has been in the Cloud Cuckoolandhell hole that is Cool World he's never been "killed" by a doodle? and he's a cop? Even though he knows that death in Cool World isn't permanent (as he explains to Lonette shortly before going back. By all rights he should have been a doodle a week into his stay!
Frank casually backhands Sparks in a way that suggests a noid is a lot more physically capable against a doodle. Plus, with one law in Cool World, how many rule-breakers are there really going to be? Frank's job is really more like "chaperone to Holli Would" than "full-time peace officer".
Who the hell IS Sparks, exactly, and what is his relationship to Holli? Is he her manager? Ex-boyfriend? Pimp? Drug dealer? Family relative? Or just a local lowlife? Also, how could he have possibly known when Holli and Jack had actually done it? And just what is his beef with Frank?
Knowledge of various Doodle/Noid interactions and their consequences are extremely widespread in Cool World, but aside from one or two throwaway lines about what Holli's been up to lately, Frank and Jack are apparently the only humans who've even been to Cool World, let alone know it exists.
Debatable as it's implied humans have lost it and come to Cool World, they usually just don't last very long.