I just did this last week on a slim 2001a model.
However, mine was not a permanent install and I shutting to think of someone taking this route, at least with my model.
Your model motherboard probably doesn't require this but I had to shave the left side of the clip were a capacitor was causing it to be millimeters up-seated. Then I wadded three nickels in electrical tape and placed it on top of the seated clip (don't tape it to the board). After this, I was able to get good backups and a successful write to the NOR. I followed this guys video for most of it.
Though again, I took a different approach with the clip. Clamps are an over kill and taping it to the board causes more harm then good (in my experience). You just need a nice fit and (light) evenly applied pressure.
I know your wanting to do a permanent install with your E3. However, that's going to be a tad unpractical depending on your motherboard. Rumor has it, the E3 clip was only designed to fit snugly on the slim CECH-25xx models.
EDIT: I did hear of people placing a small bit of packing foam on top of the clip. Then the heat plate will actually apply pressure to the clip after being put back together. Though again, this clip is a pain in the ass to get fitted right (at least on some models). It took me two hours of fussing with to get it to read correctly and I had the board exposed.