I have the stock filter in there now that's really old but seems to be working.  I would like to keep it stock but I can't locate a new air filter and I'm thinking they aren't available.  Is there a foam substitute, or does the whole air filter unit need to be changed out?  Thanks in advance. 

Dave Kolbo @ KDI makes the exact replacement filter for your CT1 

www.kdirepros.com/Air-Filter-p/248-14451-00.htm

Thank you! Right now I'm in a wrestling match getting the air cleaner joint and air cleaner on to the carburetor throat and am losing badly. I wonder if I slotted the air cleaner joint in two places if it would be a little more cooperative.

My guess is slotting would ruin the boot.

Try putting boot in hot water a few minutes and trying to install when warm. 

As Mark T said I would avoid cutting the boot as this may lead to other issues.  You might also try rejuvenating the rubber boot with a rubber restore product.  This will restore elasticity to the old rubber. 

As a side note, Yamaha issued the attached service bulletin changing the filter element from paper to foam.  

 

My original showing the remains of the foam (not paper) filter

 

Gersh has already mentioned KDI doing the replacement Air Filter element
for your bike .
They also do a replacement rubber boot between the air box and carb .
A worthwhile replacement for old hardened and shrunk originals .
The cost is justified by getting rid of the grief involved with old hard parts .