My 4 inch Gil exhaust chokes down to 3 inches at the transome. I need to either enlarge the exhaust ports, or drain off some of the water going into the exhaust. What are some techniques used to do this, and how to do it safely with rubber couplers in the exhaust system?

The best way is to install the 4 inch outlets.

I'm honestly not trying to sound too harsh here at all, but are you really sure about that??? GIL has ALWAYS made at least a 4" O.D. tailpipe and it comes standard on all their exhaust systems that way except for the GIL Big Guns which I think were 4.5" O.D.----well, I at least have yet to see a set of GIL tail pipes necked down to 3 inches unless of course they were custom made particularly for that application. Anything is possible I guess.

Yes, I'm sure about the reduction in exhaust diameter. The Gils were not stock. The prior owner installed them, using the stock 3 inch openings at the transome from the original cast iron exhaust system. The Gil parts are the manifolds and the SS risers. From there, and including the reduction, are generic exhaust parts.

I did this with my CMIs. Weld1" bungs on the top of the tails just before the transom. Then I welded 3/4 of the outlets inside the pipe closed so I wouldn't get too much water through them. Just enough water to keep the mufflers and transom from burning up.

Just use the manifolds, risers and 4" rubber exhust hose to connect to the tips. and buy some 4" tips and open up the transom holes to 4"
Junk the rest of the stuff.
Dan