Probably 5 should be 3. Some shrink tubing is small enough to grip the cord well but won’t slide over the mag end easily if at all. That’s the tradeoff making you fatten the cord up a bit.
Takes under an hour, especially if you've done this before and have some practice with the cables. Under 2 hours if you count driving to Best Buy and back to get the replacement HD.
It looks to me like there's nothing you can do to these little "black box" ports except make sure the tab for the headphone port is pressed down enough to contact an inserted headphone jack. Otherwise you'll want to get a replacement part. http://www.powerbookmedic.com/Intel-iMac... is one place I found online that seems to carry it. Thankfully it's not too pricey.
You can use one hand to hold the edge up while reaching with the other hand to disconnect cables. You may want to have a prop handy (like a small book) or an extra person to hold the edge up while you disconnect cables.
Very easy to lift the glass out. Don't jerk too hard.