Here are my recommendations.
Route -- Pune - Nashik highway. Go till Narayangaon. Take left for Junnar. Shivneri is in Junnar. Well maintained fort.
Reach early mornings @7 or 8 am. The atmosphere is really good there.
Come back to Junnar, take malshej road from Junnar. On the way you can see naneghat. Another good place to visit. From there you can go to malshej ghat. However all of this will be too hectic, though they are near by.
My suggestion--
Trip 1 : Shivneri, Lenyadri, Ojhar( these two are lord Ganesha Temples) in one day.
trip 2 : Naneghat only. Trekkers delight (not a motor-able road)
Trip 3 : Malshej Ghat
If you are going to Malshej ghat directly, cross Narayangaon, go till alephata. At alephata joint take left and go directly to Malshej ghat. By doing this you will stick to highway only.
After Narayangaon @3-4kms and before alephata there is a winery restaurant Chateau Indage. Good food and good wines too.