First I would check your connections on the battery to make sure their nice and tight, the radio freaking out sounds more like a bad ground than anything (this is a factory radio head unit right?)
The fuel mileage indicator will fluctuate for a while as you've erased the learned values on the "optimism meter" (as many of us refer to it as it is typically inaccurate), so I wouldn't worry to much about that, it will level out to what ever it thinks the average fuel economy the more you drive it.
You also need to reinitialize the automatic function of the driver's window and rear window after you disconnect the battery. To do this simply roll the window up and down 3 times in a row without stopping (going all the way down and up), this relearns the jam protection feature and lets the "Auto" function on both the Driver's Front Window and Rear Hatch Window to function correctly.
You may also have the VSC & ABS warning lights come on, this is because on the '03 & '04 models the Zero Point Calibration (ZPC) data becomes erased when the voltage drops too low (usually below 12.0volts or when you disconnect the battery); you will need to perform a ZPC relearn to correct the issue (there's some write-ups on the forum for it.)
Did you by any chance relearn the idle after you disconnected the battery? Usually Toyota vehicles run a bit rougher and shift a little worse after having the battery disconnected for a bit; the reason is that the learned memory in the ECM is erased and the vehicle needs to relearn your driving habits. After you disconnect the battery for about 5-10 minutes you want to let the vehicle idle with no loads (no radio, no A/C, no lights, ect.) for a good 5-10 minutes to let it get its bearings; after which driving it like you normally do for a while will let it relearn your driving habits.