Hi, my opinion is, that you may have a lot of possible problems.
Firstly as you want to live in CZ, first of all you need to have Rodné číslo - Czech birth registration number. Thats quite new law in CZ.
But this the point where you should start. I recommend to discuss all this with some foreigner, living in CZ.
As you will not find any contact, I can ask to someone (having Mini, born in Belgium, living in CZ).
I find interesting link
http://www.registr-vozidel.cz/car-registration/car-registration-foreignersbut as always, this is service for somebody going to register usual VW or Opel, not Rover Mini.
Possible problems may be your special car with many specific details.
As it is possible, to use your car less than 184 days a year in CZ, use present NL registration and insurance. As your car will be in garage during winter for 6 months, you will visit Netherland once in two years for making NL TUV-ASU for next two years, and thats it.
Because, before registration in CZ you should have document, that you canceled registration in NL - means
no way back.Secondary problem, I think much bigger, is:
ORV ( OTP ) se mimo trvalý pobyt omezuje na dobu povolení k pobytu - as you will not have Trvaly pobyt - Permanent residence in CZ in documents (czech document for foreigners), you will probably have Povoleni k pobytu Sojourn residence permit in CZ - means for limited time (one two years) you will have your Czech registration valid ONLY for tis limited time.
Therefore its hard to make the decision, what you should exactly do.
And I found one more specific question - I am not sure, that you can legally drive as Czech resident with czech documents a car with NL registration longer than 184 days or one year.
I was for 3 years in Berlin and I was also having a lot of problems. They ask for german driving license etc.
Finaly I made my resident documents every year from 3.1. to 23.12. so every year starts new period and I fulfil the german laws (of course always new passport). I was there with my Austin and because of Brno town registration I had BMU0315 plate and BM could also mean Berlin Mitte, so zero problems. But it was luck, with Prague car registration plate it may were other.
Or, you can legally
buy the documents from some Mini in CZ and use this metal plate (label) and use existing documents. Together with NL registration. Or overwrite the chasis number etc. There are also many possibilities.
Contact on me you can find in my profile and my skype is agmartin1
Good luck
See overview- schedule what all you should do:
http://www.hrabyova.cz/prihlasovani-vozidel-prihlaseni-vozidla-registrace-dovezeneho-vozidla/see sector A and B (not C - new cars).