Re: 1995 force 40 hp
One of 2 things.
please clarify, it won't run at all, with the cowl on?
Then look for a wiring issue, as in a wire that is being moved or pinched, when the cowl is put on.
If it will run, but not well, and not long, then you most likely have an exhaust leak. The exhaust is venting into the cowl area and starving the engine of oxygen.
Exhaust leak is usually below the block, there are a number of seals and gaskets, part numbers 6,8,12,31,or 33, in the diagram here:
http://www.crowleymarine.com/mercury-outboard/parts/1452_180.cfm