With regards to the directory names I am using folders prefixed with guids not full paths so this shouldnt be an issue
With regards to your other suggestions, do you have any urls where I can get further (and concrete) information on what i need to do - google searching is providing me with a miriad of conflicting suggestions.
Also before I read you reply I dropped the PHP version to 4.3.9 and eveything worked until a DB connection was attempted in step 2 - I assume this is due to the new password hashing mechanism that MySQL 4.1.7 uses.