I know you said you were trying to avoid it but splitting your model into smaller chunks is probably the best next step. I made a sketch on the Top plane and put a simple grid of lines on it using a couple linear sketch patterns.
You can then use this sketch with the Split feature (under 'Insert', 'Features', 'Split') to break the model into several pieces. With the mesh still set to incompatible this should be able to mesh again with the mesh completing for most of the bodies and failing to complete only in a localized region. You can further add sketch entities to split the failing body into smaller chunks and narrow it down further.
If you had the original file with the feature tree still in it the process might be easier since you could just roll back the feature tree and re-mesh until you find the feature causing the failure. Then remodel that feature. With an imported body splitting the body into pieces is still a pretty fast way to get to the bottom of the problem.