Since your low/mid speed is good you really have two places to look..
Carb and valve train..
You've been over the carb and if it's thoroughly clean maybe turn your attention to valves.
1st a set of feeler gauges and a simple adjustment..hope this make things better because if not then thing get a bit deeper.
Also while your valve caps are off check the springs carefully..a broken spring might be causing valve float and your power loss.
Next the timing chain..a worn chain might be causing improper valve timing and your power loss!!
Lastly, engine compression..gauge it and check. 20-30 psi low can feel 'good' when pulling the cord, sure will knock the crap out of your top end power.
This noise you talk about may just be more than the engine showing its age..further investigation is required!
Current toys..
1986 Honda 350X..trail bomb!
1985 Honda 250SX..my main mudder
1985 Honda 250ES..Back in Black Trike
Current non-trike toys:
1990 Honda TRX300FW
1995 Seadoo GTX
1998 Polaris Indy Lite 340(Nearly new looking)
1998 Polaris Touring 500
1998 Club Car (electric)