yes, you can save all your settings and flash your phone. there are several ways to do it. Regardless, there is a learning curve.
The problem is that if you are only going to flash once, it may not be worth setting up. I flash about 3 times a week, so just about everything is automated on my phone. I use
sashimi. Others use
user configuration. I used UC in the past, but found it frustrating because typographical errors messed things up. Others don't like sashimi because they get overwhelmed with everything it does.
As far as saving specific settings, you would need to have the reg settings set up. One trick I use is to use sashimi or another program to back up the registry. Then make the change in the program you are interested in. Then back up the registry again. You can then use
windiff to find the changes. Change the setting back to where you want it, and then you can copy the key into the sashimi ini file.
However, as mentioned previously, this stuff is only helpful if you will be more frequent flashes. If it's a one time thing, it may just be easier to bite the bullet and just do it. You can use ppcpim backup to backup the files.