Spotlight + Time Machine woes - tried everything...

Question

I have a 10.6.7 system with a 1 Tb internal drive (~700 Gigs of it used) and an eSATA external drive used as a TM destination. I make backups religiously, and I'm up-to-date with all the updates. I have a similar setup at home, with mostly the same data, which doesn't have the following problem, so I know it *can* work (and should!). But here's what I have.
This all started after exporting a bunch of old emails as individual files (~30 Gigs-worth - maybe 20,000 files all in all). I noticed that my Time Machine is taking forever to make backups. Not just the first time, but all the time, even when no files have changed (at least, at the user level). I've repaired both disks with Disk Utility, reset TM according to the suggestions in the TM forum, and started from scratch with a blank drive. The problem is this, as seen in Time Buddy:
Starting standard backup
Backing up to: /Volumes/Mercury External Drive/Backups.backupdb
No pre-backup thinning needed: 989.3 MB requested (including padding), 341.04 GB available
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Indexer unavailable (200)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
Indexer unavailable (200)
Waiting for index to be ready (100)
Waiting for index to be ready (100)
     The TM often tries for like 30-40 minutes (each hour!) and then sometimes fails with
Error: Flushing index to disk returned an error: 0
Copied 3725 files (167.0 MB) from volume Raptor RAID0.
Backup canceled.
     I don't think it's a hardware problem with the drive because this used to happen when my drive was a USB2 drive (I specifically got a new eSATA drive because I thought the extra speed might help).
    The problem seems to be that the Spotlight indexer is constantly busy. I followed directions to completely wipe out and rebuild the Spotlight (and this is after using SuperDuper to clone my drive to a completely clean disk, and using Cache Cleaner to do a deep cache wipe etc.).  The Spotlight rebuild took 2 days, and during this time the size of the .Spotlight... file went up and down. The time predicted by the little magnifying glass thing up in the menu bar went from 8 hours to 657 hours, but eventually it finished (when I excluded the folder of exported mail messages via privacy list). I already have the TM and other disks excluded from Spotlight.
    Spotlight alternates between being quiet and usable (no dot in the magnifying glass) and mds alternating between 98% and 5% in the "top" terminal command, and all of a sudden running like crazy (dot in the magnifying glass) with a spinning barberpole and no estimate of finishing, for no apparent reason.
    I've used fs_usage in terminal to determine that Spotlight was spending a lot of time on my Microsoft Entourage files, so I excluded those. Unfortunately I need it to scan my Microsoft Outlook 2011 files because I can't search for emails without it (yes, I'd love to dump the Microsoft product but I can't for now).  Now the fs_usage doesn't work anymore - it says
fs_usage: the trace facility is currently in use...
                fs_usage, sc_usage, and latency use this feature.
a reboot helps, but only for a few minutes - then fs_usage says "killed" and won't restart again (giving the above message).
   I'm at the end of my rope. What do I do? I need my disk indexed by Spotlight, and I need TM to be able to do its normal 3-second/hour backups after the initial one.   Where do I go next?   Is it possible that I simply have too many files here for Spotlight to work properly?
thanks in advance,
Mike

Answer 1

Yes, I did mean GUID. It was the TM drive. I did an archive and install, but keep in mind this was a brand new computer, that had a fresh install. Also, this all worked on the older system. I would try an erase and install, but i'd like to see if there is anything else to try first.
Just ran again, the freeze didnt happen but it did call out some random garageband instrument.
Backup requested by user
Starting standard backup
Backing up to: /Volumes/Time Machine/Backups.backupdb
Event store UUIDs don't match for volume: Macintosh HD
Backup content size: 68.0 GB excluded items size: 44.1 MB for volume Macintosh HD
No pre-backup thinning needed: 81.50 GB requested (including padding), 90.43 GB available
Waiting for index to be ready (904 > 0)
Error: (-36) SrcErr:NO Copying /Library/Application Support/GarageBand/Instrument Library/Sampler/Sampler Files/Boldt Ensemble Detatche.Samples/VI1SHDT C6-.wav to /Volumes/Time Machine/Backups.backupdb/Michael DiMaria’s MacBook Pro/2008-10-18-104514.inProgress/943A6BE5-1166-478F-8CD8-E5454EEB7F11/Macintosh HD/Library/Application Support/GarageBand/Instrument Library/Sampler/Sampler Files/Boldt Ensemble Detatche.Samples
Stopping backup.
Error: (-8062) SrcErr:NO Copying /Library/Application Support/GarageBand/Instrument Library/Sampler/Sampler Files/Boldt Ensemble Detatche.Samples/VI1SHDT C6-.wav to /Volumes/Time Machine/Backups.backupdb/Michael DiMaria’s MacBook Pro/2008-10-18-104514.inProgress/943A6BE5-1166-478F-8CD8-E5454EEB7F11/Macintosh HD/Library/Application Support/GarageBand/Instrument Library/Sampler/Sampler Files/Boldt Ensemble Detatche.Samples
Copied 1880 files (5.5 GB) from volume Macintosh HD.
Copy stage failed with error:11
Backup failed with error: 11