Drake hit it on the head. These 990's get what we call half tank vapor lock. If the fuel is below half a tank the tractor will just not run. It sounds like its doing the same thing my 990 was doing. I tuned the carb and the issue went away.There are a few posts on cleaning and adjusting these carbs over in the MTD forum.
My very first question is - how full is your fuel tank? If you measure the bottom of the fuel tank to the fuel inlet on the carb, you have little more than an inch. Now if we complicate things with poor fuel line routing and the wrong type of fuel filter, we have an extremely poor fuel flow. A lot of us experience out of fuel conditions with a quarter tank left.
Initial mixture screw adjustments are 2 turns out for high speed, and 2 1/2 turns for the low speed mixture. Float should close needle valve when parallel with the body of the carb.