OP - I've had several visas for Pakistan issued in Australia and these days you are lucky to get the six months' validity/90 day entry visa. Be grateful for that. The visa is valid for six months form the day of issues, and you can enter Pakistan at any time up to and including the final day of validity and then stay for up to 90 days (even if this takes you beyond the six months' validity of the visa). So if you cut short your time in India, even by only one week, you can make it work.
Note that you cannot get a tourist visa for Pakistan from anywhere else outside your country of permanent residence.
The road from Quetta to the Iran border truly is dangerous, so it's more than just a matter of inconvenience. The police will restrict your movements in the region, and you will have to pay for a security escort whether you catch a bus or take a car. There is a train to Iran every two weeks -- you could consider that.
It's difficult to give advice on Peshawar. It's a very interesting city, but over the past few years it has attracted more violence and suicide attacks than just about any other city in Pakistan. The advice from Pashtuns in Sost is curious but not definitive. About a year ago, a Chinese woman who was in Peshawar as a tourist was shot dead in the street along with her a local guide/fixer. But a number of travellers, including myself, have visited the city alone and without any special precautions and have enjoyed ourselves. So I would neither recommend that you go or recommend that you don't go.