I bought one of those kits to sleeve the wires in a computer and i must say it was a time consuming task. There are some parts of the task that are a pain, but what fun would modding be if it was easy?
It would be a good idea to purchase a molex removal tool too help you complete the task. Without the tool, putting on the sleeving is considerably more difficult.
To keep track of the wires, i took a permanent marker and marked one of the black wire's end(there are two on a molex connector). Then i marked the corresponding hole that it came out of. One piece of advice, make sure you have the connector correctly positioned when you reinstall the wires. If you don't, you'll have to take it apart again, turn the connector over, then reinstall the wires.
I used a hair dryer to shrink the heatshrink tubing. It took some time but saved me $45 because i didn't have to buy a heat gun.
Finally, i would like to add this about the heatshrink tubing. I used it on about 90% of my wires and i wasn't really satisfied with my results. The ends were kind of loose. I went to Home Depot and found some electrical tape that was the right color (blue in my case) and used that instead. I think the tape looks and works better, but thats only my opinion.