Wow. 26000? 26000 namespaces, types, and members...!? I haven't checked, but my intuition is that's much larger than the entire .NET Framework.
By my math, if you'd started coding this monstrosity sometime during the early .NET betas, you'd have authored an average of 20 to 30 new types/members, each day (including weekends and holidays). And with full documentation... bully job!
Sarcasm aside -- can I take it this is some kind of autogenerated API? You may wish to skip NDoc, and generate the .html files yourself, at the same time (and in the same manner?) you're generating the actual code.
What happens if you try to compile the intermediate results of NDoc into a CHM file manually, using HHC.exe? Does it still complain about the 10 min. timeout?
(The command line syntax of HHC.exe is trivial -- just point it at the HHP file emitted by NDoc.)