The question is too general, since different coutnries may have different permanent residence permits (both regulated by EU or local laws), therefore my answer is first of all related to Germany (since the question mentions it as an example).
In such cases, I would (and actually I have already did it) get 2 permanent residence permits in Germany first:
I'm afraid you're out of luck.
The law (Act on the Residence of Foreign Nationals, in Czech only) provides several ways to bypass the 5-year minimum in § 66. Two of them could theoretically apply to your situation:
for reasons worthy of special consideration (§ 66, (1) b)
if your residence is in the national interest of the Czech Republic (§ 66, (1) c)
Is there any way that a lawyer can help me to build my case and claim the residence, or is this a hopeless situation?
Yes, continue living in the country for another 2.5 years, after which you will meet the legal requirement for obtaining a permanent residency and then apply for it like everyone else. Unless you're a truly exception scientist who's known ...