Obviously, a solid-state hard drive would be best, but I've never had any issues with my spinning platters. I have a piece of rounded-edged lauan I cut just larger than the laptop to ensure sufficient airflow and I place the laptop on it and it on a folded-up towel in the tourpak. It's easier to v-tune well with a remote display placed in easy view but it's not necessary. Just ride with deliberate throttle action avoiding sudden change as best possible.
It seems a lot of folks like to disable the accel enrichment and decel enleanment for the v-tune data runs but I like to leave them enabled. The argument is that it enables a greater number of hits while gathering data because whenever the two functions come into play then data gathering ceases for several seconds as the temporary changes decay out again. The argument is also often accompanied by the statement that the data doesn't get skewed with the functions disabled, but it's also been commented how accel enrichment can be greatly reduced from the base calibrations when done tuning. I haven't done any comparisons between both ways but have a gut feeling that when accel enrichment is disabled for v-tune data gathering that a little bit of it gets "built in" as a result. I'm not looking to start up another discussion about it, just mentioning my position. You'll be able to pretty easily find and read the other side if any of it matters to you.
So long as you follow the text of what's in the manual you fetched from mastertune.net you'll be okay. I believe there's a flow-chart near the end that slightly differs from the main-body text, so unless you ferret out the differences just go by the text.