1) I believe you can get the controller from Masterbuilt support directly. They tend to connect with just a single cable, so swapping them out isn't a problem. You may also consider bypassing the builtin controller / thermometer for a PID, which can give you better temp control. On my MES 30, I use one from Auber Instruments.

3) For the wood tray, I would recommend looking into the "mailbox" mod that's popular on these smokers. Some 3-inch flexible duct work, a couple of elbows and a mailbox and you've separated the smoke source from the heating element, letting you do cold smoking, or use something like the A-Maze-N pellet try to smoke for hours and/or add smoking material without having to open up the door.