Flaps- Yes, you can not deploy them if you are above their rated speed.
.speed - This command defines the speed the "auto speed" (an auto pilot function) will maintain. To activate autospeed press alt-x. The plane will then adjust and hold a climb, or decend angle required to maintain that speed. By defult, it is already set to maintain the best climb rate for the plane you are in.
Throttle - If your joystick has a separate throttle...Try and recalibrate your throttle, but do not move your throttle all the way to full position during calibration (say only to 80% or 90% for example). That way after calibrating, the whole top 10% range of you sticks throttle will be full throttle, and it should stay at full throttle then.
If it doesnt have a separate throttle slider, maybe you could be more specific on exactly how you have it setup so we can figure out what might be your best option.