I wouldn't worry about your botched switch. It is almost certainly not going to be a problem in getting the game running. Once you have the game working and you are making design choices on the retheme that is when you want to decide if you are going to use the same square yellow targets or something different.
If you do decide to use those yellow ones i have a bunch of old switch stacks you can have. I can bring them to the cleveland pinball show if you happen to be going to that.
Also good to mention it is easiest to get those switches clean and straight when they are "dangly". I always burnish the contacts and flatten the switch leaves out before mounting them back on the playfield. If you make the switch look as close to straight and flat as possible it will probably be gapped correctly once new rubbers are installed.