Keep the mountain pedals and shoes for a while. You will need to dial in your bike position and saddle first - no need to add another variable or two with new shoes and/or pedals. Once you are happy with the other things - you can change if you want - or just stay where you are. Minor changes in shoes and cleats can make a big difference - I switched from Shimano to Look cleats/pedals (same shoes) and it has taken me a month to get them just right - I had aching knees for about 3 weeks.