It might be the 2002 Korean anime Chaechaepong Kimchipong, as in these earlier questions:
This anime seems to be one of a kind in terms of stuff almost entirely lost. No episode can be found on the Internet to confirm how much it matches, several people search it with no success (here on 9GAG), someone even claims the original Korean dub is lost (link).
Proving that this may or may not be the anime at stake is then based mostly on the recollection of former askers (see links at the beginning of the post), and bits from the opening:
- Magical girl, check. Her hair is pink, I don't know if her look is what you'd remember as "something odd with her hair".
- I tried various translation services on this wiki page (in Korean), and all state that Tochi avoided becoming a stone because something something large stone tower. Literally what I get from Google Translate is "Torch, who accidentally acquired Kimchi Stahl in a large stone tower, escaped from becoming a stone alone without knowing the English."(?), and Systran gives me "In a large stone tower, Tochi, who accidentally holds Kimchi Stahl in his hand, is free from being a stone, without knowing English." (??)
Point being, that stone tower may be a well, or the recollection of a well might be a mistaken memory of a stone tower.
- This (0'22 in the opening) vaguely makes me think of a fruit-sized glass "sphere".
- There were bits with food being taken out of a device to summon creature powers in the earlier questions.
- So was it being broadcast on MBC3, and the main character having a yo-yo (your "telescopic handle tool" maybe? Or the device unfolding at 0'46 in the opening?).
What would not match is the "mad scientist"; if I am to believe the summary above, and this one, the villain is the evil Lord Aegross (curses, not science). I'm also not sure whether the girl's mic-looking device (wand?) can shoot like a cannon.
In the most peaceful village on Earth, Singleland, a boy named Tochi lives a normal life with his grandmother. One day, all the creatures that lived in their land are suddenly petrified, leaving Tochi as the lone survivor.
Bewildered and frightened, Tochi meets a travelling little witch named Milo who informs him that what happened to his village, and many other villages including her own was due to the curse of the Black Mage Army. She reveals that he wasn't petrified because he had the magical Kimchi Stalks, therefore she gives him the "Chae Chong", a summoning tool, which only the person with Kimchi Stal can own. The "Chae Chong" can summon a Kimchi Pong when you put a Kimchi Stall, a powerful magical creature, which they use to fight the Black Army.