I haven't built a Mack so I can't help you on that but when you bought the plans you got free tech support. If you call the number on the plans or web site you get to speak with Frank or Tom and they are 2 of the best at designing and building smokers. So don't hesitate to give them a call, you'll be glad that you did.
Something is amiss on the angle iron not fitting properly, Frank is usually pretty good about working out all the details properly so if you have something not fitting it is definitely a good idea to call him. Nice guy and has always gotten really good feedback for his guidance.
The warped side is another issue. The angle iron frame is used to seal the door so needs to be square. If your side is already welded in and you are sure it is the side (and not the piece of angle iron) that is warped, I’m not sure you can do much more than just weld the gap shut. You might get lucky and pull it together a bit with a pipe clamp but be careful not to bend the angle iron. There is also a 'process where you repeatedly apply local heat with a rosebud and then mist it with water to pull the warp out but it requires a pretty big torch set, some patience and a lot of time.
Otherwise...looking like a great build.
Bigger question is where did the warp come from? Was it there in the plate already? Too much heat from cutting it or welding it? Might be a procedure change needed to help prevent it in the future.