I have also had my share of problems of installs and re-installs of SHIII. I now have a workaround that works for me.
I have a clean and patched to 1.4 stock version on my computer. I leave this installation as is.
If I want to create a modded SHIII version I just copy the stock folder and place it on the HDD under another name. You can then mod this copied version as you like. Right now I have stock, GWX I and GWX II version of SHIII installed.
If you manage to foul up a version, you can easily delete it and start a fresh project by just copying the original folder again.
Concerning your inability to patch: you might want to take a look in your registry; problems with reinstallations in my case were caused by still existing SH III registry keys. After deletion everything worked fine.
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Daddy cool 
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