Repeating problems (1) Many Missing Files; and (2) Downloading From iTunes

I am having multiple issues with the iTunes store currently. I have spoken with an Apple Expert on August 14, 2010 (case number available if needed). Although he was very good at helping me to the best of his ability, he referred me to iTunes Store Customer Service, which I previously was in contact with.
I have 2 types of repeating problems (1) Many Missing Files; and (2) Downloading From iTunes Store.
_Problem One - (1) Downloading From iTunes Store_
I have 1610 missing files from my iTunes folders. I created a list of missing items by following these steps:
+If for any reason you find yourself with random missing tracks, (or are trying to recover from a dying hard drive like me), there is an easy way to isolate those missing tracks.+
+1. Create a standard playlist called "Not Missing".+
+2. Drag your entire library into that playlist. Missing tracks cannot+
+be copied to a playlist.+
+3. Create a smart playlist called where you select the following conditions in the options window for the new smart playlist:+
+*dropdown menu* PLAYLIST+
+*dropdown menu* IS NOT+
+*dropdown menu* NOT MISSING.+
+4. Rename the smart playlist "Missing"+
+5. Right Click the "Missing" playlist+
+6. Click the "Export..." option+
+7. Select the Plain Text option and Desktop location+
My missing playlistable items represent a better part of a decades worth of audiobook files, transfered files from my PC days, etc... i loved my - now missing - Doctor Who and Torchwood purchases from iTunes.
I have already read the Trouble Shooting, checked Time Machine Backup, and been walked through replacing the preferences list. The missing file path from the "get info" options in iTunes points towards a non-existant file.
_Problem Two (2) Downloading From iTunes Store_
I have had problems downloading files from iTunes for months. I first noticed it with the TV Show "Avatar: The Last Airbender". Lately, when I download from the (non-music) part of the store, the majority of files are downloaded and then immediately not found. This has been prompting iTunes to repeat the download. Until I force quit itunes and *potentially cry*.
There have been multiple iTunes store purchases of audio books recently. If I reported the missing file immediately, I can contact iTunes support to repost the file and that usually fixes the issue. But today, I went to go rewatch "Torchwood: Children of Earth" and noticed Problem One.
_Hind Sight_
If provided with a spreadsheet of my iTunes Store purchase history, I can write a vlookup( formula in excel to compare the list against my exported missing list so a shortlist of what is missing from just my iTunes Store purchase history can be created (hint: it's the majority of items from the list, others are years worth of files from my PC days). If we could do that, could iTunes make my missing purchases available?
Then we can focus on purely, trying to figure out why they went missing in the first place - so we can prevent it again & possibly help others from running into the same.
Plea
I strongly suspect the two issues are related to a root cause ... in addition to my user error in file management of backups ... what is going on?

iTunes Support (Eric) emailed me some instructions. I am posting, in hopes that this will help others.
_Suggestions from iTunes Support_
Troubleshooting 1. iTunes Store: Finding missing purchases and downloads http://support.apple.com/kb/TS1408
Troubleshooting 2. Direct Assistance
_Results based on Suggestions_
Results on "Searching the harddrive" - did not resolve my concerns
Results from "Direct Assistant" - i emailed the list of the missing files... status is pending
Conclusion
I'll follow up again later, if I have new news.

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