I like how there are two ways to say "I have a headache" in Japanese, and they are written with the exact same Chinese characters, but are pronounced completely differently:
頭が痛い (atama ga itai)
頭痛がする (zutsuu ga suru)
you think that's cute?
harakiri (腹切) is seppuku (切腹) backwards
Also in Chinese, "我有頭痛", tho "我有头疼" is often used in mainland speech.
"我有頭痛" sounds very Taiwanese. This usage of 有 is an artifact of Taiwanese / Minnan dialect. The Standard Mandarin (普通话) way to phrase that sentence is just "我头疼" or "我头很疼". Also like you said, 疼 sounds a little more mainland and 痛 sounds a little more Taiwanese. A general word for "pain" is 疼痛, they are really synonymous.
It's pronunciation that's hard to guess from kanji.