If you would have to go out and buy some, its good enough - but let it dry completely. Also look at the ingredients, make sure there is nothing but alcohol and water. Some "rubbing" alcohols have a little oil in them.
Before I get flamed yes 90% + would be much better but jeez guys its not like its being put together in a clean room and shot into space. Most of the "carrier" for thermal compounds is a synthetic oil anyway.
Personally, I buy the toughest, single-ply John Wayne, tough as nails and won't take shit from anybody, toilet paper and use that. It's more lint free than q-tips or other TP's like Charmin or Cottonelle. Wipe away as much of the old thermal grease as you can with dry TP, then finish up with the alcohol. Letting it sit for a good 10 mins should be enough to ensure a dry surface. Once clean keep your fingers off the IHS surface so as not to contaminate it with oils.
Thats pretty much it....oh...and remember to stay grounded while doing this.