1) Are they okay to you? Functionally/physically, they'll very likely be fine. It depends on how you feel about the cosmetic factor of them. It sounds like they are not original but what truly matters is if you care or not as it is your game. Unfortunately to change these you have to disassemble/remove the entire pop bumper assembly which I am not sure I would recommend to a newbie, especially because this can mess up how well the switches are adjusted/how well the game plays. If you are going through the game you would likely have to adjust these anyways. However if you are going to be doing anything to this game that is one of the easier things you can do so while I would not recommend it if you could avoid it, I would say go for it otherwise actually.

2) People fill in these dips when clear-coating entire playfields but that is likely way out of your league both because of the process (especially with the added task of filling in inserts) and also because you have to disassemble everything on the top and bottom of the playfield to get it down to the mechanically-bare wooden playfield board. I haven't experienced cupped inserts myself on my own games (it is a fairly common issue though on others' games it seems) so I can't really speak of a different remedy for this myself, somebody else may be offer more insight, I am not sure if there is another good way. You may be able to find reproduction inserts with the art on them or decals of the art to stick on new ones but I have never liked replacing inserts as they always seem to be stark white and look weird when the art ring that slightly overlaps them is gone.

A GREAT game by the way, I don't think I've played one yet but I've seen a lot of pictures and it is a beautiful game! Have fun with it and good luck.