You bet I do! I have always made all my fleece accessories and have learned along the way what works.....at least for me. I doubt that you will ever be happy with the combination of items that you are trying to put together and trying to sew them will be a nightmare....as you've discovered. You asked for it, so here it goes.
First of all, you don't want the liners to be waterproof. Their purpose is to absorb any type of liquid, not repel it. Towels are the absolute worst item you can use in a cavy cage because they get wet, stay wet, and smell........quickly. Instead of wicking away the liquids, they hold them in. The whole purpose of using fleece over an absorbent layer is to wick the liquid AWAY from the piggies so that they stay dry.
A great many of us use uHaul pads which are superb for the middle absorbent layer, and you can't beat the price! The pad is 68" x 85" - $7.95, washable and durable, made out of recycled denim. One pad should be enough to make liners for a 2x5 cage with a 2x2 loft which is what I have. Do not inadvertently order the "moving blankets" as they are terrible for the intended purpose.
One caveat about using the uHaul pads....you MUST prewash them in hot water and then a hot dryer to have them maximally shrink BEFORE you sew them. Fleece shrinks only slightly if at all, and you don't want to painstakenly sew your beautiful liners only to have the middle layer shrink and leave you with bunched-up pads. I shrink the pads and then press them to see precisely what I have left to work with.
Fleece also needs to be prewashed in order to make it wick.......as in wick down to the middle layer. Fleece is generally coated with products to make it somewhat waterproof.....which you don't want. You need to strip that waterproofing for the intended purpose. Don't get discouraged because you might need to wash the fleece several times in hot water with detergent and maybe a tiny bit of bleach. How do you know when you've done enough? Lay the washed fleece on an absorbent layer (now is the time you can use your towels) to ensure that it is indeed wicking the liquid to the under layer.
Also, when measuring your liners, make them at least an inch larger than the perimeter of your cage. Despite perfect preparation, the liners will still likely shrink a little with time.....and leave gaps around the edges. Somehow virtually anything not nailed down will end up in those gaps, and that most often is poops.
Once you have everything prepped and cut and are ready to begin, sewing is actually the easy part. It's good that you have a walking foot, but you don't really need it. I have found that one layer of uHaul is sufficient although others use two layers. I found that makes them more difficult to sew and they take longer to dry. I am still using liners that I made eight years ago and can tell that they are worn out because the middle layer (uHaul) has likely disintegrated with time and they leak more than they absorb. Some people just use separate layers of fleece and uHaul, but I can tell you that the uHaul pad will disintegrate far sooner if it isn't encased in fleece. Insofar as the finished liners go,
never dry them with any type of fabric softener or dryer sheet as that just coats the fibers once again and will cause them not to absorb properly.
I use incontinence pads under the liners. I have used all sorts of items including puppy pads which are temporary and not good for the environment, plus cavies can spot the blue plastic and just love to eat it! I'll list some incontinence pad sources below. With these, you sew the desired dimensions BEFORE cutting the pad or else the layers will separate and ruin your project. Sew to the desire dimensions and then cut close to your stitching lines. These pads last far longer than I ever expected and just get tossed into the wash along with the liners, cozies (aka cuddle cups), pads, etc.
Many folks here on the Forum sew their own liners and will probably have more information to add. My guys desperately need new liners, but I'm a busy professional who just doesn't have much time to sew. I have yards of fleece that I bought two years ago on Black Friday that are still in the shipping box. Hopefully all of the links work, I haven't had time recently to check them. Most of all, have fun and let us know how things go.
https://www.uhaul.com/MovingSupplies/Packing-Supplies/Furniture-Pad/?id=2670
Incontinence pads
(broken link removed) (34" x 36")
https://www.amazon.com/gp/product/B003QSDFL4 (35" x 80"
How to Make Cozy Sacs and Cuddle Cups
https://www.youtube.com/watch?v=FSXmzaMC5OU
https://www.youtube.com/watch?v=uo-6KOTOvmY
https://www.youtube.com/watch?v=ssTSLs9hW0k
https://www.youtube.com/watch?v=ut7jC4FZFtw
Cuddle Cup Tutorial
https://www.seamshappy.com/2012/01/19/cuddle-cup-tutorial/
How To Sew Fleece Liners
https://www.youtube.com/watch?v=Ub37uBfZ3lc
https://www.youtube.com/watch?v=T1YyABZZS58
https://www.youtube.com/watch?v=FSJe7FA1BkA