I have a 2000 Tundra limited. After having the in dash 6 disc player replaced 5 times, I gave up, went to future shop and bought a $140 JVC in dash deck that supports MP3 (on disc) and also has a front mounted mini-rca AUX input. This AUX input would work great for your MP# player. Also because the new unit is only approx. 2.5" high, and the stock unit was 5-6" high, they installed a plastic storage compartment which is ideal for a wallet or your external MP3 player.
Regarding properly mounting your MP3 player, do a search on RAM mounts, they make 3rd party auto mounts for everything from laptops to cell phones and GPS' units.
Cheers,
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