On the Beneteau 43cc, they don't come close to having the problem we have. The engine on the Beneteau is mounted above floor, whereas on the 49 it is below floor.A friend's Beneteau 43 CC has very similar problem with the same Yanmar engine. We were able to pull the pump cover plate with a small ratcheting 90 degree screwdriver (http://www.harborfreight.com/8-piece-right-angle-screwdriver-92630.html) then using a long 90 degree pliers,(http://www.harborfreight.com/16-inch-long-reach-pliers-set-38598.html) grab the impeller and by tapping the pliers rearward, we got the impeller out.. Not an easy job, and can't be done on a hot engine.
He'd bought the official Yanmar impeller puller for the engine and it did not even come close with the restricted access.
Note that on the new models of the engine, the pump faces forward and is actually accessible.
That means that the sides are totally inaccessible. Still, your buddy had a nasty time doing this.'
I agree that a right angle ratchet is a good tool, but I have an additional idea. In all spaces where it is virtually impossible to easily access screws, I change them over to socket head cap screws. You can buy stainless ones in any thread & length.
The advantage is that they are Allen key drive. So, the first trick is to use a bit of masking tape to hold the screw onto the Allen key. Now, it will go anywhere you want without dropping it.
Once you start it in the hole, there is nothing easier than an Allen key for positively driving in a screw.