If your pet door is adjusted as small as it can go (with extension pieces) and it is too tall to insert into your track, there is a simple solution.
Install your extension pieces as per the instructions, however leave one of the extensions on the support bars, but not screwed in place. Now push that loose extension piece up and right into the one above it. Now you should be able to fit the patio pet door into your track. Once its in there adjust the adjustable top all the way up as far as it will go. Tighten the thumb screws to hold the adjustable top piece. Now you need to pull that loose extension piece down and out of the one above. You should then be able to align the loose extension piece in the correct spot and insert the screws into place.
See this video here for a brief explanation. I have used a black extension with a cream door so you can see the two parts easily.