"MINWAX" makes a kit to repair rotted wood. It is simple to use and contains a wood hardner for the salvaged section and a wood filler, basically bondo, that you use to build up the area. The filler is a little thicker than thick pancake batter and starts to harden at a steady rate. You will have to make a mold/dam of thin plywood to hold it in place as it hardens...about 30 mins. Wax the inside of it so it will release...I used beeswax. You'll need to have a fill area across the top of the mold for pouring it inside. You can touch up the fill area when you remove the mold for a smooth finish...remove any wax from the repair.
Another method is to use epoxy L&L resin and any medium/fine sawdust to make a stiff putty that you shove into place w/a putty knife. You have to work w/it quickly due to set up time being quick. L&L resin comes in cool weather and warm weather types. It's a sticky job but fills all voids easily and holds the tube in place. Most boat product vendors sell it in some form. They also have a 2 part epoxy putty you can use.