Yes a C6 will bolt up, but remember that the E40D is an electronic trans and your PCM controls it. When you install the C6, you may have to install a PCM from a manual trans or your engine light will forever be lit. Also, if you have ABS, it may require some work too. The drive shaft will be different. The Xfercase may not bolt up ect. When you finally get it all sorted out, did you save any $$. I would check your local Ford dealer, some trans techs will build them on the side. I usually can get one built on the side for $800-900. Some of your bargain basement shops may get as low as $1k but you get what you pay for from those shops.
A C6 is an E40D without the O/D Section and Int is a band in the C6. So they are real close in structure. Where are you located? I may be able to help you further <img src="/forums/images/graemlins/wink.gif" alt="" />.