Writing and posting overlap here, so I'm not commenting on immediately preceding posts...
You said that you would first do domain redirects and then do the redesign process with changing url structure. Wouldn't that mean that I would be again redirecting previusly already redirected links from .net and that original redirects on those links would be lost this way?
I mention this in my post, where I suggest "avoiding chained redirects of inbound links on those pages that are affected."
Multiple changes are going to be an issue either way... ie, whether you do the domain redirects first or whether you do the redesign first, you will still have the potential of chained redirects to deal with.
Doing the domain redirects first gets the alias domain out of the way asap, so you're not picking up additional links to the .net, so offhand seems like the best way to go... but one could probably argue it either way.
With either approach, though, this is where you'll want to carefully check backlinks and carefully note which links specifically are important to "preserve", as you will have to go back and make changes in your redirect rules the second time around to avoid "chaining".
Note that you should set up your DNS so everything is going to one
IP... the IP address of your .com. You won't be setting up separate redirects on your .net hosting account to redirect to the .com. You'll be using only one .htaccess, eg, that's on your final domain's web hosting space. This is an important point. I'm not understanding your specific DNS and WHOIS concerns, because I don't know your hosting is set up now, and because the questions aren't clear... but keep in mind that you should have only one hosting space where you do all your mod_rewrite work.
Also, fwiw, the current estimate on what is lost per redirect is about 15%, so in two redirects link credit won't be entirely lost, but you should try to avoid that loss if possible.
Some of the comments I make in this thread, along with the thread references in my section post, might be helpful.... Links or 301 Redirects - from Old to New Site? http://www.webmasterworld.com/google/4172816.htm
There's been a more recent discussion on multiple redirects, which I'll dig out if no one else finds it.