How to convert a muffin/cupcake recipe to a large muffin recipe
This table comes from the front of the muffin section in Bread, by Beth Hensperger:

Muffin size          Baking time     Yield
Mini/gem (1 5/8")    10-15 minutes   18-20
Regular (2 3/4")     20-25 minutes   9-10
Oversized (3 1/4")   25-30 minutes   6-7
Muffin cake (8-9")   55-65 minutes   1


The baking times are for 375-400°F; most recipes will fall around that range. Note that the yields don't necessarily match up to typical pan sizes; for example, if you take a recipe meant for 12 regular muffins, you'll probably have more batter than you need for a pan of 6 oversized muffins. Perhaps this is your problem - you could be overfilling. If even after scaling the volumes appropriately, you still have problems, you could try reducing the temperature by 25°F and increasing the baking time.

("Muffin cake" refers to baking in an 8-9" pan of some sort - the author says that you can get away with it for any muffin recipe, but I've never tried it!)