Even before Partition, the only district with a Hindu plurality was Tharparkar with 49%
Thaparkar was 80% Hindu before partition, and the district borders India.
Immensely doubtful. Local leaders would be begging India to take over the region - anything to keep the Muslims out - and as with Kashmir, India would accept. Furthermore, having heard the terrors of Partition from firsthand account, and having seen Hindu refugees coming in with injuries and talking about dead loved ones, a Hindu mob would likely try to lynch the Pakistani soldiers in an attempt to avoid the same fate.
If Pakistan sent troops into Junagadh if India still decided to go and attack Junagadh they would have to fight them as well. While they could easily defeat 500 troops, it will lead to Pakistan being even more forceful about Junagadh, and I doubt India was going to engage in a rivalry with Pakistan over a small princely state with nothing unique. Kashmir, which India was willing to do that, was not as small and had an abundance of mineral resources. If India was going to engage in a rivalry with a country that (used to) had a chance of attacking it on both fronts, India was not going to do this with Junagadh.
So, they’d create colonies akin to the Ulster Plantations or the West Bank settlements
Colonies? In that case, Karachi is a Uttar Pradeshi and Bihari colony. Note that when Bangladesh was East Pakistan a law was passed which gave the government permission to confiscate property of Hindu refugees, which continued when Bangladesh became independent, and it was only recently repealed. Why it couldn't happen in this situation, I don't know. As Junagadh begins to lose their Hindu population, Muslim refugees would begin to enter (an unofficial population transfer?). It happened before numerous times in India, where multi-religious cities such as Lahore (which was a holy city for Sikhs, yet they still left, much to the chagrin of the Shiromani Akali Dal whose leader Tara Singh shouted "Pakistan Murdabad". If Lahore could become a majority-Muslim city due to Sikhs leaving despite objections of Sikhs why couldn't Junagadh become Muslim-majority despite objections of Hindus?), Karachi, Dhaka and Amritsar with the first three then becoming >90% Muslim and Amritsar becoming >90% Sikh because of partition.
Furthermore, having heard the terrors of Partition from firsthand account, and having seen Hindu refugees coming in with injuries and talking about dead loved ones, a Hindu mob would likely try to lynch the Pakistani soldiers in an attempt to avoid the same fate.
I don't know why you put this here, or how this is relevant at all. Yes, maybe some Hindus might attack Pakistani soldiers, though the Pakistani government is smart enough to know that those weren't ordered by the Indian government.
Nehru cared little about Kashmir.
Nehru said he had a "partiality to Kashmir", and was willing to make it an issue even when the forceful Patel was willing to give Kashmir to Pakistan. Even if it were not the main reason, it can not be denied that it wasn't a factor. Since in Nehru's own words he was biased, he'd care more for Kashmir rather than Junagadh.