I would remove those links if i were you.
I have the delrin top Supreme HF (all black). To be honest the top is'nt going to make much difference to the temps. The only gain would be from the nickel and full copper ones but even then it would be tiny. Personally i don't like plexi tops as it's too easy to crack them when tightening the barbs up.
You will have 9 screws to hold the motherboard down all of which are probably a phillips/posi head screw. When fitting the new board do not overtighten them as just a pinch is all that it required. You should'nt have to move any of the motherboard standoffs as the new board should have them in the same place.
First step (after removing the loop) would be to remove the graphics card and any other add on cards.
Next undo all the power/usb/sound/sata/front panel wires from the mobo. Just tuck them out of the way, no need to remove them completely.
Then undo the screws holding the mobo down. Remove the mobo and put it to one side. If you have the original packaging then you should have the anti-static bags for everything. Remove the rear I/O shield as the new board will need a different one.
Remove the cpu from the mobo, clean it up and place it in it's packaging. Place the black slot protector over the mobo's cpu socket to prevent any damage and pack it all up.
Now would be a good time to have a clean out of any dust in the case.
Now to put the new board in.
Take the socket protector off the new board and insert the new cpu the correct way around, there should be a little arrow in one corner of the socket which lines up with the gold arrow on the cpu. It's easier to do this now than when the boards in the case.
Fit the new I/O shield to the case.
Fit the new mobo and make sure the holes line up with the standoffs then screw it down. Just a pinch remember.
Connect up all your cables and power plugs etc. The cables for the case should have a little arrow or triangle on the plugs. This means positive (+) and should be put the right way around. See your new mobo's manual for the correct layout.
You can now put your graphics card and any other cards back in.
You are ready to stick your loop back in now.
The only difference would be if your case (what one is it?) does'nt have a rear cutout on the motherboard tray to access the backplate for the waterblock. We can sort that out if the problem comes up. Hopefully your case has the cutout.
I never use a anti static wrist strap and have never killed a component yet. Just make sure you do the build on a table or something similar. Don't go doing it on a carpet and don't take the components out until you are ready for them. Placing them on their cardboard boxes would be ok but don't knock them over.