I have three 2" and one 3" roof vent stacks where after only 10 years the rubber boots are failing allowing water to enter the house. I noticed that Builders Edge makes a Stack Cap expressly for such a fix, but it only comes in a 3" to 4" size. Do you have any suggestions to fixing the leaking boot short of replacing the entire stack cover and roof shingles? Are you aware of a replacement device that might cover the existing boot, thus preventing any further leaks?

I don't know about any new style roof jacks but I would suggest replacing them with lead jacks ,cost more ,but last three times longer than rubber jacks. Depending on how old your roof shingles are, there are pretty simple to replace. You might have to cut pipe off for the lead jacks ,because they cover the whole pipe.

They don't come in 2" because vents should not be 2', you sure have a lot of vents too. You could try to build up the 2" stack with several sizes of PVC and cement. The lead collars do last a life time.

Shingles are not too difficult to remove and re-use. I replaced 3 rows x 15' of shingles this year. A crowbar is essential.

This glue which is clear can be used to fix any shingles.
Sashco Sealants - Through the Roof (http://www.sashcosealants.com/Home_Improvement/Through_The_Roof.aspx)

These guys make a thinner viscosity in a paint can and can be used with a "patch" to repair ripped shingles

RF-140 Black Magic, Roof and Flashing Sealant from
construction adhesive manufacturers - adhesives - sealants - OSI Pro-Series® (http://www.osiproseries.com)

can easily repair the shingle bonds.

I took off the shingles using a crowbar and a large putty knife. Repaired the tears. Plugged the nail holes. I also was able to patch the tar paper that was exposed using the "through the roof" and a piece of tar paper as a patch.

The real problem arises when nailing the last row back. I put a large flat piece of steel, like 4" x 4" on top of the nail head and attempted to start the nail. Then I put the shingle back and placed a large board, say 8"x10". I hit the board, which would go through a shingle, through the large piece of metal and driving the nail.

I really didn't have much trouble. I did end up with a whole row of shingles left because I replaced it with a starter strip.

You guys have to look harder: 1.5, 2, 3 and 4" sizes

https://keithspecialty.com/dwv.rubber_fittings.htm

Lowe's sales an 1 1/2 to 3" boot that you cut to fit what size pipe you have. they also sale 3" and 4" as well

As for the origianal post you can try and use black lap sealant for now until you need to replace the whole boot,
As for replacing the boot its not really difficult, to do, but I wouldn't advise you do crawl onto your roof unless its something your comfortable doing

I have 2" lead boots on my house right now & if you try fixing it with roof cement it will be harder to replace later