1-2) The both are correct but the way of saying “ Ayasofya İstanbulda.” is informal and it’s a speaking way. In Turkish generally writing and speaking is not same. While speaking we ignore the grammars but in writing grammar is necessary. In Turkish grammar the predicates should be end of the sentences. And predicate indicates a certain statement so yeah they mostly end with the suffixes like “ -d(ı,i,u,ü)r .
3) as long as you want to mention the location of the thing and want to emphasize where is there then yeah. For example; Telefon masanın üstündedir*
5) mi-ı-u-ü? Are question marks. If you say hastene burada it means “ the hospital is here” and if you add —mı?-Hastane bura da mı?-> is the hospitality here?