Time is money too. The time that it takes to install the boots is worth for me more than the new boots -I recall they costed me about 60 bucks or so-. I doubt there are aftermarket boots either. Aftermarket companies normally specialize in "consumables", you know, brake pads, cables, filters etc.
If you install the engine sides first, you will have four mouths for the carbs. Dont' tighten anything. Squirt a little WD40 in the carb throats and in the rubber boots, twist the boots until they are aligned, with the bike on the centerstand -it helps if you tie a strap from the centerstand to the front wheel-. Put the carbs facing the boots, tilt the carbs slightly downwards, and once the four mouths start to enter the boots, make a big press with the carb setup. Once all four mouths are in it is a matter of evenly pressing them. Don't tighten anything. Do the same with the airbox-to-carb, bolt the airbox in place, and once everything is in place start to tighten the clamps.