Bought a used 1999 GS500E over the winter and tried to start it today and it wont start.

I am new to this model so please cut me some slack.

Here is what I have done so far.

Put fresh gas in.
Checked plugs for spark
New Battery
Tried like crazy to start it

Here is what I discovered. Some items could be nothing but figured it best to give all the info i can.

When I open the left carb drain I got very little flow and than it stopped. Even after cranking it still never flowed again. The other carb was fine
When I pulled the tank off to drain it I noticed gas did not flow for both inlets. The longer inlet flowed fine but the shorter one did not only a few drops.
After desperation set in I sprayed some starting fluid in the plug holes. It fired immediately but would not say running after the fluid was burned up.
Also when I pulled the tank there was along hose laying on top of the motor. It is the hose that connects to the T connector on the carbs. Looks like it might go in the painted fitting under the tank. I cant find it the connection point in the clymers manual it only shows where it connects to the carbs.

Sorry for the long post I am just stressed.

Any idea or insight would be greatly appreciated. Thanks in advance.

If you aren't flooding it, then it souds like your carburetors are gummed up.  I'm going on it being the latter.

I've never taken these puppies off my bike to check, but many here have.  I'm sure someone will chime in and add their insight soon. 

But in the interim, if I were you I'd begin to check the feed lines, going from the carbs back to the tank.  (Make sure you're on PRIme on the petcock.)  If the feed is good, yet the plugs aren't wet, then the hang up is in the carbs.

I think some checking & removal can be done with the carbs in place.  If I guess right the bowls are accessible, and if you remove them you may have a sense of how varnished the fuel delivery system is.  If it doesn't look pretty, I'd swallow hard and remove the carbs for a complete cleaning and reset.  You could use a solution of GUM-OUT or similar additive and hope Chemistry is with you, but this may just be wishful thinking.

You're out of my experience at that point.  Next opinion please...

Yep it sounds like you have gummed up carbs. You said that you already have a manual so it should be easy to follow the diagram. Basically you just neet to take everything apart, clean it with carb cleaner and put it back together.

Clean the jets by soaking them in solvent and blowing through them with compressed air (don't use a wire)
The only part in the carb likely needing replacement is your float valve, but it's probally fine.

There are two lines going to T fittings on the carbs, one is your fuel supply, and the other is your float bowl overflow, and it routes to near the right peg. (check your diagram to make sure you have the supply going to the right one.)

The painted fitting on the bottom of the tank is your tank overflow (it goes to the little hole under the gas cap) there should be a hose on this going to near the right footpeg.

The reason that fuel only came out of the one tank outlet is probally because your fuel level was low and so it only came out of your reserve outlet.

Put the petcock on prime to get the thing started. Once it's running you can switch to the ON position and leave it there, but whenever your carbs are empty, you need to start it on prime.

Good luck 

Thanks for the help it is greatly appreciated.

Also don't bother trying to start it untill you have a steady flow of fuel out of your carb drain when you open it and have the petcock in the prime position. If you don't have fuel going to your carbs, you need to make sure the fuel lines are hooked up right (check your manual) and that the carbs are put together right and not plugged up.

I'm having a very similar problem. I'm going one step further & replacing the fuel lines as well. One of them seems to have completly deteriorated at the tank connector & I'm sure is attributing to the problem. Mine is an '04.