Instead of converting a pair and having it look a bit messed up you can easily do a manual fit with shoes and boots.
1. Zero Aiko after you load her. The option if found on the Parameter Tab option menu when she is selected. You can make it a Tool Bar button for easy access.
2. Load the boot(s). Depends if they load together or not.
3. Position the boot so it kinda lines up with the proper leg.
4. From here you may need to start scaling and repositioning the boot further depending on the boot.
5. If the boot is a knee high boot then you may have to hide A3’s Feet, Toes and her shin either from the surface tab, the scene tab or both depending on the boot.
6. You will need to parent the boot to the proper part of A3’s leg. If it goes over the knee then you should parent to the Thigh. If its below the knee then parent to the Shin.
7. If the boots load together such as TreadZ then for each leg you will need to hide the unwanted boot.
You may need to use magnets or d-formers to help with the odd poke through.
Only real down side I can think of is that if you are not very accustomed or comfortable posing your own characters, then this makes posing A3 anoying at best. Have patience though, its worth it.
In this image here - http://mattymanx.deviantart.com/art/The-Pose-5-204187164 - I used the OverKnee Lace-up Boots for V4 by DX30 and hid A3’s legs and parented to the thigh. I noticed that the knee bend in the boot lined up perfectly with A3’s knee BUT, you cannot see her legs so only the boot got bent!
In this image - http://mattymanx.deviantart.com/art/Toon-Raider-103774369 - we see Staci by 3D Universe wearing Aiko Toon boots (by 3DU) Those boots load together instead of one at a time so there is actully two pairs of boots in the scene.