A local shop you use might be willing to give you money and/or better credit towards future work -- good if you have another bike needing work in the near future.
Craigslist or any other local outlet will be better than ebay, since the buyers can come and see what they are buying. This forum is likely to be the best venue since we know the relative fair value of the bike/parts. You may not get the absolute top price, but you are more likely to not waste your time with flakey buyers who lowball you. Depending on the parts involved, you might want to part the aftermarket stuff out (especially if they are valuable or new) and then sell the remaining titled frame motor and other stock parts together.
If you have a higher end project, sell those higher end parts (e.g., Mike Rieck ported head, modern forks, APE crank, Wiseco kit) separately. "Projects" will most likely yield a steeply discounted price.
