Does anything exhaust out the chimney (is it being used or future use with existing fireplace)? If no, remove chimney just below decking and redeck (have to get to rafters (so will have to cut bigger hole)). Install felt and shingles. No more issues or future leaking. If yes, use Bill's suggestions of mortar, stucco or framing and save the money. Home Depot can show you how to install the metal flashing to replace the old and protect your hard work.
Do you have pictures you can share? I have a roofing company and can share my opinions from 1300 miles away.
Bill is also correct on prices of shingles. Most manufacturers will increase prices just before the building season (March time frame for KC). Often we see 7-10%. Some local suppliers will discount at the end of season to get rid of inventory - odd lots, not as popular colors.
I have also been on customers roofs that look old and shingles are old, but don't need to be replaced (even though other roofing companies told them it had to be immediate). Pics would help.