You have two options:
1- Trim the bottom of the doors: This is not a good idea in my opinion, because the bottom part of the frame will look different the sides.
2- Trim the doors at the top, re-adjust the hanging mechanism.
Well, I've decided to go with option #2. If you remove your doors, the hanging mechanism looks like this for the inner door:
That brown piece that is held by 2 screws is what is hanging the door on the rail, and that piece simply slides left/right on the rail. Re-Adjusting this inner door is relatively easy. You simply 1- unscrew the piece 2- drill new screw holes 3/8" (or whatever your adjustment is) below the original holes 3- screw in the piece in its new position. 4- Cut 3/8" wood from the top of the door. Otherwise the door will hit the ceiling and you won't be able to fit it back in. Here is a quick picture of old and new holes..
Outer door is a bit more challenging:
Note that the plastic hanger piece is in the inner face of the door, and the wood steps up about a 1/4". If you just repeat the steps for inner door, it won't work. because the rail will not fit between that step-up and the new position of the hanger piece. So, you actually need to trim the step up by 3/8" too. How will you do that? I used a circular saw and vibration cutter combination. First of all, you draw a straight line 3/8"below the step-up. Then you adjust the depth of your circular saw to the height of the step-up, and cut through the line you've drawn. Now you need to put in the flat blade in your vibration cutter and take the strip of wood out by sliding the vibrating blade under it. Try to stay within 3/8" of an inch, but it won't break anything if you go any further.
See the pictures below.
Important things to note:
-Be very careful with power tools. That blade doesn't know the difference between lumber and your finger.
-If there are any staples on your way, take them out before you start cutting. You don't want to cut through those, because it may kick back your blade and create a dangerous situation.
- Note that each door has two plastic hangers. Make sure you don't switch their positions, because they're not quite the same. The screw holes are not identical, and you'll have serious alignment issues if you accidentally switch them. Ask me how I know...
Anyway, your next task is going to be figuring out how to install the metal guide on your new flooring..