Well that will certainly work if you're in a hurry, but if it were my project I'd look for a saw that cuts on the pull stroke, like this one:

http://m.homedepot.com/p/DEWALT-Double-Edge-Pull-Saw-DWHT20216/205436902#

I discovered Japanese-style saws maybe 30+ years ago, not once looked back.

For cutting thin plywood, particularly if it's got fiberglass epoxied to one or both sides, these saws will cut vastly more efficiently with less splintering / tearing than Western-style push saws.

 http://www.japanwoodworker.com/

Lots of options here over the big-box stock. Christmas is coming too!

While several people have successfully cut their take-aparts in half with a Japanese style pull saw, some people have also regretted it.  John specifically describes the saw to use in the plans.  My manual is at work, so I can't quote him at this exact moment, but he uses a Western style saw with teeth that have no offset that cuts on the push.  The Western style blade is thicker and stiffer so that it wanders away from the cardboard "bulkhead" less.  

A Japanese pull saw is very thin, flexible and cuts extremely well, so there's really nothing stopping it from slicing right through your pretty keeper bulkheads. The common comment is that the pull saw cuts so smoothly, you don't feel when it's cutting through the bulkhead.  Yikes!  

I'm a big fan of pull saws, in fact I cut out the entire hull of my EP with one by hand instead of opting for power tools.  In this regard, I'll rely on John's advice when it comes to cutting my PMD in half.  I figure he's cut dozens of boats apart in his life, who am I to second guess that on my first attempt?

I didn't see anywhere on the link that it specifically states any info about the tooth offset.  The fact that it says it's non-binding makes me think it does have an offset, to create chip clearance.  A saw with no offset might be more prone to binding if you were sawing through solid wood, but for this operation, you aren't.  By the time I get to cutting my boat in half, I'll have so much invested that buying a $30 saw for a single use to ensure the success of the operation is a no-duh, slam dunk in my opinion.  

Having read CaptScully's posts I'll withdraw my recommendation. This is obviously one of those times where experience at a specific task outweighs more general experience gained in more mundane endeavors.

Only time I've ever need a saw with no "set" has been when cutting exposed thru tenons where the tooth set likely will mar surfaces better left untouched. Alternate teeth are set only to one side, the others left "setless" thus minimizing the chance of scratching.

Facing bulkheads - two of 'em no less - is more demanding so take heed.

Now as to finding a western-pattern push saw with no tooth set may take some time. This forum post may provide some insights:

http://woodworking.stackexchange.com/questions/927/what-is-the-purpose-of-a-saw-set

If you can find a saw having a tapered blade you may be on to something! That would be my choice, less chance of binding in the cut.... perhaps even going so far as to file off the tooth set on both sides for this particular purpose. Done with care the result may be sharper than as-bought.

Assuming those facing bulkheads have been separated by a slight clearance, cutting thru thin planking ought to require minimal effort with little chance of the blade binding, which is why saw teeth are set in the first place.

Checking Stanley's website for more details on that particular saw turns up that it has induction-hardened teeth so don't try filing the set off those, they'll be too hard.

http://www.stanleytools.com/en-us/hand-tools/cutting-tools/saws/26-in-sharptoothtrade-fine-finish-saw/20-065  

   Woodcraft.com has a good selection of Japanese pull saws. They also have a link at the bottom of their home page for another site where you can buy hand forged saws (japanwoodworker.com?), but they are very expensive. I have a pull saw I got at my local hardware store and it was fine.