Hello,
If you don't mind long drives, it will be no problem. It is also closer to 3 1/4 or 3 1/2 hrs, one way. Your plan to do both sides of the Bonavista Peninsula is a ggod one.
I would recommend you drive direct from St. John's to the Bonavista peninsula turn off at Clarenville. You could drive out through the Conception Bay Highway from St. John's through a string of small communities but it would add another hour or so to your trip.
I would recommend for scenic drives, stops....Trinity, Trinity East, Elliston (with a visit to Puffin Rock, which has a good vantage point for whales and puffins), Bonavista Lighthouse (great vantage for scenery, icebergs in season), and Plate Cove area. Also beautiful is the drive to New Bonaventure, past Trinity.
For lunches, you can check out the many inns in Trinity, The Twine Loft is a good choice or Two Whales in Port Rexton or a new spot in Amherst Cove called The Bonavista Social Club. Although I personally have not been to this last spot, it has excellent reviews with a focus on breads prepared on site.
Hope you enjoy your holiday!