I'd make sure you flatten everything out really well. Glue some paper to a piece of glass, a granite block, or even just a piece of 3/4 MDF or anything else you have that's reasonable flat. Take a pencil and shade the mating surfaces before sanding them flat. This will help you see if you have any high or low spots anywhere.
As for using the pins again, I'd probably just cut new pins and leave them a little proud so you can peen them. You don't want to over peen everything too tight, but a a little bit of peening will help to fill the minor gap that appears to be around your pin in the first picture.
If that wood's not stabilized, you're still likely to have some gaps down the line regardless, as temperature and humidity changes.