I found that if you take the retaining clips off and compress them a little then slide them back into position, they tend to stay in place better and line up with less difficulty. And the advice to use minimal pressure while re-bolting will help a lot too. It sucked the first time I did it but once I figured out its little idiosyncrasies it wasn't quite as bad.
As for the seat, I've been eye-balling the Corbin gunfighter. Most people have said it's a fine seat but the customer service is awful. Waiting to see if Sargent will make a seat for the newer models. They will also do custom but very $$$! Great customer service though; I've heard.