My project was created in Xcode 3, I\'m opening it in Xcode 4 and notice the following:
EDIT: It seems that if you have any custom header search paths to support multiple targets with shared code XCode 4 indexing will break and then assistant and codesense along with it. I have raised this as #ID 9182099 with Apple. There is also an issue that if you have any conflicting settings between project global and target specific build settings the index will fail to complete correctly. Make sure that your build settings are consistent.
I have just had this problem in a very large, multi target commercial project. As an additional pain all of the xib files would not show the controller in assistant view and none of the subclass/superclass/siblings/categories assistant views would work either.
After much searching and experimentation with deleting the indexes etc I was forced to create a new empty project and re-import everything. I know you have said that your project is too big for this but I dont think there is any other option available. In the end it has taken me most of a day to migrate my project completely. I suppose you could hold on hopefully for a resolution in a future point release but I chose to bite the bullet now to benefit from the productivity increases from the new features.
To achieve this I created a new "empty" project and then manually recreated the targets I needed. I then deleted the source and .plist files for the new targets leaving me again with an empty project with the three targets I needed.
I then just selected "add files.." to the project one folder at a time linking against target as required. I stopped and built each target as it was imported to deal with any compiler errors that the latest clang gave me.
If you have a complex group hierarchy that is not mapped to a file system folder structure then you will either need to recreate the groups after import or go through the painful process of moving all your files into subfolders and re-pointing the references in XCode.
You will also need to carefully check any custom build settings in the targets as well as relink any libraries you include. Also make sure you remove any bulk imported .plist files from the target linking.
Sorry if this is not the answer you had hoped for.