Because the handle that I attached the desk to are about 5 inches long, I cut the first section of my desk supports to 5 inches. An ordinary hand saw will cut PVC very easily. Use some sandpaper and/or a knife to remove the burrs from the cut surface. If the cut surface is going to be exposed on the completed project you may want to round the edge a bit so that it won't be so sharp. Dry fit two of the 45 degree angle pieces on the 5 inch pieces and slip them in place.
Using the 45 degree angles as a guide, measure the length needed to provide adequate clearance for your legs and knees on the bike. When measuring you may want to consider others who may also want to use your desk and bike and design your desk appropriately.
Cut the risers to the length indicated by your previous measurement and dry-fit them into the 45 degree angles attached to the handles. Dry-fit the second pair of 45's on the top ends of the risers.
Cut two more support pieces to attach to your wooden desk surface. They should be about the same length as the desk. Dry fit the desk supports into the 45's at the top of the risers. At this point you should be starting to get an idea of where the desk surface will be. As you measure, be sure to allow for the length added by the 45 degree angles. It is a good idea to sit on the bike and hold the complete dry-fitted supports in place to determine that everything is coming together correctly. Do not put any weight on the dry-fitted pieces at this point. The PVC joints will not be stable and will not support and significant weight.