[Transformer TF300T Q&A, Help & Troubleshooting] EndlessDissent:
I know it doesn't help, but since you wanted to know what happened, I can tell you that much. Since you were on CM9, you had to be on the original ICS bootloader. Stock JB can't be fastboot-flashed over ICS because of changes to the partitioning and other low-level stuff, which is why it wouldn't flash and why it subsequently failed to boot.

I'm also just picking up my TF300 for the first time since August. I just recovered from a soft-brick today (my story, which in hindsight was a complete f-up on my part), which was why I hadn't been using it. I ended up fastboot-flashing the newest ICS firmware (I actually tried it back in August, but fastboot wouldn't work; I didn't do anything differently today, but fastboot had been updated recently and magically worked), then performing the NVFlash backups from the sticky thread (this isn't quite where our paths diverged, but it may have been a good idea to do that before you tried upgrading to JB -- not that it helps now, but for future reference).

Like you, I tried fastboot-flashing the stock JB firmware over the ICS firmware and got the same error you got. So, I tried flashing the ICS firmware again, but got the same Invalid Size error. At this point, my tablet wouldn't boot past the splash screen (not the animation with the spinner; the first one with the NVidea logo in the corner), and fastboot wouldn't flash any firmware.

This next part is the part where our stories more-or-less fork.

Faced with another soft brick just hours after fixing one, I fastboot-flashed TWRP instead (made sure to use an ICS version since the JB firmware didn't flash, and the NVFlash bootloader I had was based on the ICS bootloader), which worked, and I booted into recovery. I used TWRP to flash the ICS firmware (I actually had it on my internal SD card in August, but I could have also pushed it with ADB if I didn't already have it), and I got a functioning tablet again.

Next, to upgrade to Jellybean correctly, I booted into Android and used ADB to push the Jellybean firmware to my tablet. I put it on the root of the internal storage, and the tablet saw it and alerted me to the update. Since TWRP had been replaced by the stock recovery when I flashed the ICS firmware, I just let the tablet do its thing with the update, and I ended up with a perfectly-functioning stock Jellybean ROM. I then performed each subsequent update (I never once skipped any update steps) the same way until I was on the newest 4.1.1 firmware (I'm not updating to 4.2.1 until CM10.1 works with it).

I'm not sure how much research you did before you updated your tablet, but I was trolling the TF300 forums for a good 2 or 3 hours before I even tried upgrading, and I still had trouble (I never saw any posts about people trying to fastboot-flash JB over ICS, so I didn't know it wouldn't work until I tried it at least 3 times). From the limited details you provided, it doesn't sound like you did much searching before you started flashing. In the future, it may be a good idea to research a lot more than you think you have to before flashing things on expensive devices.

Also, in the future, when you're asking for help like this, it's best to go overboard on the details - just like a murder investigation, we want to help you figure out what killed your tablet, but we can't do that if you don't tell us about the strange footprints you saw in your neighbor's lawn the night before. Mention every single icon or word that appears on the tablet, every single button-press you've made, every keystroke you've typed, etc., whether it seems important or not. We can't be there with you, so you have to bring your situation to us.

At this point, the only advice I can give is to let the tablet die, charge it again (so the battery's full but the tablet's powered off), and try again when the battery's full. If you can get ADB to work while the tablet is trying to boot recovery, you may be able to flash a new recovery and then try flashing the ICS firmware (flashing the JB firmware might work, but then you can't use NVFlash). That's about the best you can do if you can't get it into fastboot mode (short of RMAing your tablet). If you can get fastboot to work somehow, then you can easily flash a new recovery and follow the steps I took. But if you do get your tablet booting with the ICS firmware, perform the NVFlash backups ASAP before you update to Jellybean.

I hope you can get your tablet to work. I thought mine was a goner until I got lucky with an updated fastboot. Now, I'm ecstatic that it works, and I'm going to be a lot more careful in the future.