Pheonix, a couple of tips that may help you.
Check if your tuned pipe is blocked by blowing through it (you might want to wrap a tissue round the end first - unless you like the taste of burnt castor)
You should be able to blow fairly easily through it. If it is steel, then you can use drain cleaner in it for a few days, then rinse thoroughly. Don't try this with aluminium though!! It will dissolve it. For ally pipes, you can use the splayed out end of a short flexi drive in a SLOW electric drill. Put a tube over the flexi to stop whipping then hold the tube and feed the assembly through the pipe as a sort of rotary brush.
Tuning should not be done either on the bank or held in the water. The loading when running is far less than when static in water, and far more than running in air. Also the engine is getting little, if any, water through it so can easily overheat.
The best way is to get it running steadily but rich at 1/3 to 1/2 throttle, then launch the boat (having first checked the throttle and rudder are functioning. Drive round in a circle without touching the throttle then,
when the boat is passing you slowly open the throttle (this way, if the engine cuts, it will be close to you for retrieval). I suggest you invest in an old fishing rod, some strong line and a tennis ball. Fasten the ball to the line then, to recover the boat, cast the ball over the top of the boat and haul it in
If you absolutely MUST try tuning when holding the boat in the water, push the nose of the boat down so that the prop almost clears the water. This will reduce the load on the prop so you will get a slightly more accurate setting - but this should not be done for long even if you have some cooling going through the head.
You can make 1/4 turn adjustments and repeat the process until you are happy. It's a pity you haven't a local club with an IC guy as it takes longer to describe the process, than it does to do it.