Does it matter much which size you get? Is one size more universal than the other?
I have them both. I find the only difference is in the feel of it, so, personal choice...
[EDIT: Realize I didn't address the question you asked, but the question of "which is better for replacing the stock stem?" If that's all you are doing, then either is fine, will feel more sturdy/solid, and seems to produce better results (as reported from the people that have tried both). If you are looking to do that AND use the GonG with other equipment, it rather depends on what you already have as to which would be the better choice.]
Wipe down with qtip/alcohol - charge for 6 hours and do 2x 20 min burn offs at 430?
That sounds good, but as Turk pointed out, might not be necessary. But if it gives you peace of mind...
I will note that if you have stealth, to beware of ISO around the middle panel. One member caused their panel to bubble a bit, although that might have been when it was hot??
As the other 4 styles are printed, and not that rubbery material, they should be fine.