First i would like to applaud your quest for knowledge.
This is a very long topic, i will try to summarize as best i can and break the discussion into to parts. Pukhtoons and Balochis.
NWFP (now known as KPK) was conquered by the Sikh in the early 1800s and became part of Punjab after that the British conquered it and were under their control for almost 2 centuries. During this time we got acclimated as part of British India. And when the referendum was called for Partition, the Pukhtoons voted to join Pakistan. And now 70 years as part of Pakistan KPK has prospered significantly mean while Afghanistan has gone from bad to worse. So basically we choose to be part of Pakistan and weren't forced into joining.
As for FATA joining Pakistan as it wasn't really part of British India. The Jirga had decided to join Pakistan instead of Afghanistan.
Secondly Pukhtoons have not been punjabified. we have been urdufied. Pukhtoons have now totally integrated as part of Pakistani fabric. There are more Pukhtoons in Karachi than any other city in the whole world. We are happy because we do not get discriminated against and thats why you will find Pukhtoons in every field from military to sports.
Its the similar situation with Balochis, majority of Balochistan except the Princely state of Kalat had voted to join Pakistan. The map below shows the Princely state of Kalat (RED) with-in Balochistan
View attachment 419216
Now after almost 70 years Balochis have integrated into Pakistan but they havn't had the same opportunities to grow as NWFP due to their corrupt Sardars and incompetent/visionless leaders of Pakistan, but thats a discussion for another day.
As for your statement that Balochistan should be part of Iran, i do not agree and the reasons that Pakistan has twice as much land of Balochistan (347,190 km²) compared to the Irani state of Sistan & Baluchestan (181,785 km²) and Iran itself is facing issues of Balochis wanting independence. Also even Afghanistan has a small territory of Balochistan (Province of Nimruz, Southern Helmend and Southern Kandahar).
Hope that helps with your quest to understanding the situation.
You say you Pashtun voted to join Pakistan.
Then what is Afghanistan and it's Pashtun?
How did the line get drawn.
And what was the basis of partition of Pashtun.
Cheers, Doc