Been reading the 1988 CR250 reed cage info Hoser has on the home page. Can you use the intake boot that goes with it to easily fit a 38mm carb in as well? Or are the dimensions wrong for use on the FL350 as far as air box fitup?

For the 350 you cannot, the air box will not line up. Use the stock OEM intake to fit the 38mm carb, if you look at the tech pages there is a thread on immersing the intake in boiling water to heat the rubber, then expand it to fit the carbs inlet. I use an old shoe stretcher to do this mod and it works great, but just heating the rubber in water and actually spreading the rubber by pushing the carb into it will work, just be patient. It takes time. But will be fine for the 38mm carb. The cr 250 intakes work well on the pilots, in fact in some cases better then the stock OEM intake but not in the 350.
Mossbarger Inc still makes a intake for the 350 you can buy that fits the larger carbs, up to a 41mm if my memory serves me. They are in NJ and make a quality product, used them on my 350 for years and the reeds bolt nicely into it as well:

http://mossbargerracing.com/product1.htm

Tech page for doing this mod is here:

http://www.pilotodyssey.com/39mm.htm

That link is for Pilot as well as 350, in fact the intake pictured is for a 350 air box. Works the same on wither as far as heating the rubber.I recommend the Mossbarger intake as it allows you to install multiple carb without the heating and saves you the stock OEM intake in case you sell and wish to keep your upgraded carb. Just pull the Mossbarger intake and carb and install the old OEM back. Just my opinion thought.

Also IMO do not use any type of air box mod that requires removal of it. Look into keeping the air box and doing a pre filter set up like many have, the aftermarket set-ups do nothing IMO but allow dirt to get into the intakes and carbs, thus entering the Engine and doing damage to the piston and rings in some cases. Use stock air box with prefilters eliminate most of those issues.
Might wish to look at my personal PPE thread in Mudbogger's world-it shows a great bracket with dual air inlet mod I had my fabricator make-or look here for a much easier method of installing a dual air inlet mod using the stock box:

http://www.pilotodyssey.com/350air.htm

viewtopic.php?f=34&t=9292

Hope this helps you out some.