There is no way to get aftermarket speakers in with out modification, the speakers in your Avalon are made my JBL specifically for the car. 5.25" speakers fit in and work great after some modification. All you need to get a $35 dremmel tool and some bolts. I did a write up of how I did mine which you should find helpful. I put component speakers in but if you forget what I wrote about the crossover and tweeter you should be fine.
As for the sub in the rear deck, much like the speakers, it's specially made for the car. Unless yours is blown I would keep it.
Put 5.25 componets in my 98 XLS (PICS!!!!)
This guy put more simple speakers in, there not in flush and I wouldn't recommend doing what he did but this should also help you if you really want to go for this project.
New Audio System On 97 - It's Easy
E-mail me at
SpaceAlert@hotmail.com if you have any questions, I would be happy to help