I was having the same problem with the App Store and iTunes apps crashing after getting the loading screens. I used redsn0w to JB my 3Gs and everything has been smooth. I didn't have any crashes during the process and have been able to modify the themes without a hitch.
The only thing I did that wasn't necessary was in regard to mobilesubstrate. I didn't realize I needed to add the source to find the program so I installed a Voip program that I thought would handle the mobilesubstrate issue. It didn't, and I finally realized that I needed to add the source for mobilesubstrate. Once I did that I was able to proceed with Winterboard and had no issues.
I realized last night that the App Store and iTunes were crashing. They are the only apps doing this. Not knowing what to do I looked at the packages I had installed and saw the Voip program. Remembering that I didn't need it, I removed it. I didn't remove it for the purpose of fixing my App Store and iTunes crashing problem, but lo and behold, it fixed the problem.
I don't know if any of the above helps you or not, but thought I'd mention it.
Good luck!
Mike