how do you know what is the valid row, and what is the invalid row(s)?
the order a row is inserted inot a db has no intrinsic value or sort order, it is how the db stuffs the data into the db. if you want a specific order then you have to expressly tell the db what order you want when you extract the data using an order by sub clause on your select statement.
assuming this is a one off..
I'd be tempted to stuff the data into the db making certain there is an autonumber or some other form means of identifying what the original sequence is. then identify what the duplicates are, get rid of 'em, then put on your unique constraint. I'm ussing your current allpha sort order is beacue your primary key is an alpha one.
another trechniquer mya be to write a data take on programme, that load data, checks for dupliocates, applies any corrections /deletions as required.. however this will be a lot slower than a bulk file upload.
as to whether you apple gets hot or not that sounds more like a problem with that specific box. either the device is defective (so you may need a new iFan, or perhaps some iCables), or you may need to opent he box up and make sure the cooling system isn't clagged up with iDust