Sure, I'm happy to provide some guidance for your journey.

Best Time to Visit:
The best time to visit these places would be between October and March when the weather is pleasant. Note that these locations receive a significant number of visitors during festival seasons.

Route and Accessibility:
If you start from Nashik, you can take a bus/train to Shirdi, from there take another bus/train to Aurangabad, and finally from Aurangabad, you can reach Pandharpur. All of these places have good road connectivity.

Altitude and Acclimatization:
All these places are on the plains, so altitude sickness isn't really a concern here.

Accommodation and Booking:
All these places have a wide range of accommodations available, from budget stays to luxury hotels. Always make sure to book in advance if you are visiting during peak seasons or during religious festivals.

Clothing and Essentials:
Lightweight and breathable clothing should suffice for most of the year, but do carry a light jacket or sweater as the nights might turn chilly during winters. Comfortable footwear is a must as you might do a lot of walking in these places.

Health and Safety:
You should carry a first-aid kit for any basic medical needs. Stay hydrated, and be vigilant about personal belongings as these places can get quite crowded.

Local Etiquette and Respect:
Since you will be visiting religious places, tone down your attire to respect local customs and religious sentiments. Observe silence in the sanctum areas and be mindful of the prayer timings.