Put a towel down in the valley between the heads to keep any gunk from falling in there. That's called the lifter valley. Then.. yes.. scrape clean. Spray cleaner on rag and wipe surface.
Yes on doing valve cover gaskets. Although..I'd suggest you clean your surfaces of the LIM and heads, clean your bolt threads for the LIM bolts, get the sealant you are going to put on the bolt threads ready.. put a blob of RTV in the corner where the Head meets the block (4 corners) then put your gaskets in place, another blob in the corners again and sit your lim in place. Now apply your sealant to one bolt at a time and put in all 12. Hand tighten in a criss cross pattern starting in the middle and working your way outward. Then torque them to 15ft lbs if you have the aluminum gaskets, 13ft lbs with plastic gaskets.
Once the LIM is all set. Then I'd move on to the valve covers. Clean the surfaces, put your new grommets and gaskets in places, torque bolts to 87 inch lbs.