Heat up the filling before you put it in the pan with the pastry--this will keep the pastry from getting soggy. That's what Cooks Illustrated recommends and it works well.

Take the puff pastry out of the freezer on Tuesday morning and put it in the fridge. It won't thaw all the way through but it won't take so long to thaw in the evening. Maybe 20 min out of the fridge, and it will be usable?

20:52 here - I wouldn't add the puffed pastry until Tuesday. I use Pepperidge Farm frozen puffed pastry and the box says once thawed use within 24 hours. That's if OP is using a similar product.

Absolutely make it ahead of time. Make the filling (every recipe I have uses cooked chicken, and rotisserie chicken is fine). Top it with the pastry and put in fridge. When its ready to cook, brush the top with an egg wash and bake as directed, allowing for some extra time to warm it through from being cold. If the top starts to get too brown, just put a piece of aluminum foil over it.

Yes, I would make the filling and put in the dish you plan to bake it. I always use rotisserie chicken in mine, but you can cook your own chicken ahead of time (poached or roasted would be fine I think). Then on Tuesday take the dish out like 30 minutes before baking to warm up a bit. Make sure you remember to thaw the puffed pastry, put on top, and heat it up! Just remember it might take a while to warm through.

I want to make chicken pot pie, with a puff pastry crust, for guests on Tuesday. All I'll have time to do that night is reheat it (ideally not from frozen for an hour+). How can I make it ahead? I'm thinking I can make the filling on sunday & just leave it in the fridge? Should I use cooked chicken? Then just add the thawed pastry crust and bake until the crust is brown & it's heated through

sounds simple now that I type it out Hopefully it is!