Well I'm now turning to the GS gurus as I no longer have any idea what to do, basically I bought a gs500 as my first big bike and it was a non runner at the time, since then I bought a second hand engine and got it working HOWEVER it wont go past 70MPH and keeps bogging, violently jumping and loses power.

I have tried the following:
stripped, cleaned and changed carbs
replaced spark plugs, HT leads, coil leads and coil caps
used PRI
bypassed the diaphragm so that the fuel is a direct feed
checked all loom wiring
changed air filter to k&n LB and rejetted to 17.5/72.5/142.5 and it loses more power and spark plugs still seen to be running lean
checked compression
checked both cylinders are running
restricted airflow to the stock filter using a sock over it and 3 socks inside (improved performance by 15-20mph)

All of this leads me to believe it is fuel related, however I cannot for the life of me figure out what is causing it and what I need to do to fix it, I'm guessing it is due to the mixture being too much on the air side, should I just keep increasing the main and mid jets? could it be that fuel still isnt getting into the float chambers properly?

Any ideas or help would be greatly appreciated

Sounds kind of like you've routed the carb breather hose to an area unsheltered from the wind.  That problem turns up at those speeds while unnoticed at lower speeds.

Check your float levels, and make sure that your carb breather vent tube isn't blocked. Also clean out your gas cap vent. Do you have an inline fuel filter? If so, it might be getting clogged as well.

Running lean at WOT isn't always too small of a main jet (although you might try a 145).

Hey Docker.  Did you ever get a solution for the loss of power at 70mph?  My 2006 is doing the same thing.

Docker's answer:
In the end I adjusted the carbs to the point of just before overflowing, put an inline fuel filter in and made the fuel a direct feed

Quote from: joseph_dumas@yahoo.com on February 02, 2014, 08:31:52 PM
Hey Docker.  Did you ever get a solution for the loss of power at 70mph?  My 2006 is doing the same thing.

You might want to send him a PM.  That way he will get an email.