I had not heard from the dealer since I emailed them, so I called them today. Not a big deal, I've been out of town anyway. First talked to my salesman, who said he couldn't talk and would have a manager call me ASAP. A couple minutes later an assistant manager called.
I went through everything I had said in my email, and he was very apologetic and acted very willing to make it right. He said the new 3rd SCV cover was on order already, and they had a loader in stock that they could swap out for me. He told me they could pick the tractor up in the morning and return it before the end of the day. The only thing I'm not sure of is if he intends on replacing the whole loader or just the mounting posts. If not the whole loader, I'll ask them to sign a statement that I can keep on record that they chose not to replace it, even though I was afraid it may be damaged. I'll also see if they can throw in a 50hr service kit for my troubles.
On another note, the dealer said they cannot buy the cover with the slot already cut. Said it has a line marked where to cut, and they have to do it themselves. We'll see how it comes out the second time.
Sounds like I may not have to fight to get them to make it right. I'll let y'all know how it turns out.