To answer you queries one by one:
1. Best time to leave Karachi, in my opinion, is 4:30AM.
2. Best route from Hyd-Suk is to leave M9, turn left to Jamshoro on Indus Highway, take the exit (upward U turn towards right) from Aamri, This will connect you to N-5 (National Highway) at Qazi Ahmed. Please note that this road is under construction, so a few patches here and there are still not paved and for a few kilometers, the road is dual carriage. I've travelled both on N5 and Indus Highway for this route, and I prefer Indus Highway as the road is relatively new, has less towns on the way, and easily saves about an hour's time.
3. Royal Taj Restaurant at Moro is best for your 1st (or 2nd) stop depends on your driving style. It is on the right side just after you cross the Moro Toll Plaza, and there's a U turn in front of it.
Any Dhaba near Sukkur, or the rest area at Uch Sharif is a good place to take rest and food.
4. There are a few rest areas operational on M5, the best was at Uch Sharif when I travelled back in August last year.
5. Yes, there are few petrol pumps operational on M5 including Uch Sharif. But my advice is to re-fuel at Sukkur, just before entering M5. There's a fuel station right there.
6. Can't help out here as I've got no experience of hotels at Sukkur. But honestly speaking, if you leave Karachi by 4:30AM, you will be at Sukkur around 11AM or maximum by 12noon, with a tea and/or breakfast stopover. Why would you like to stay overnight?
7. M5 is full of animal carcasses, which means that they are rampant, however, please note that they usually come after dusk till before dawn. Dogs are mostly seen on N5 near towns, and foxes, and jackals are mostly seen on M5. But if you leave Karachi by 4:30, you will reach Hyderabad by day break, and cross Aamri after sunrise. From Sukkur to Multan is a 3-3.5 hours drive, and from there to Lahore (M4) is another 3-3.5 hours (the times are from toll plaza to toll plaza). So the chances of any unfortunate animal related event is minimal.
I left Lahore around 6:30AM for Karachi, there were many carcasses of animals on M4, and I saw a Jackal in the middle of the road but it stopped as it also saw the car coming as it was just after sunrise. Later on, there were none seen as the sun had come out totally. I hope it helps
