You've noticed something on the MPGuino board getting hot, and things aren't working. Here are some common problem items and matching solutions.
If the regulator gets hot, it's trying to regulate too much power. There are only a few reasons for this.
Almost all automobiles have 12V electrical systems, but maybe yours is odd or there's something wrong with the connection. Measure the power and ground connection and make sure it falls between 7 and 24 volts.
If the output is shorted to ground, you're trying to sync an infinite amount of power, this makes the regulator understandably warm.
Measure the resistance between the bottom two pins of the regulator (or any 5V and GND point). You should see several kΩ or more of resistance! If your seeing only a few ohms or zero ohms, look at the short to ground page.
If the regulator is warm, and it's not shorted, and the input voltage is sane, the regulator may be bad. With 7V or more applied to the Vin connection, measure the voltage on the regulator output, if it's not 5v, you likely have a bad regulator.
These is just a plain 7805 regulator in a TO220 package. Almost all electronic stores (even RadioShack) carry them.
The ATmega168 contains current limits on all outputs when sourcing current. This greatly limits the scope of the problem.
Measure the voltage on each pin of the ATmega, if any of them are over 5.1v, note the pin number. Most likely it's pin 4,5, or 23. Check the soldering of the 100K resistors and Zener diodes.
It happens, make sure the chip lines up with the silkscreen on the board.
Check the resistance between all outputs and +5. None of the outputs (pins 2-6, 11-19, 23-28) should have a zero resistance to +5.
Measure the on pin 7 and 20. Both of these should be roughly 5V. If they're higher, check for shorts between Vin and +5.
If either of the 1N4004 diodes is getting noticeably warm, something is amiss.
This diode protects the MPGuino from reverse polarity on the vehicle connector. If it's warm, too much power is being drawn through it, check for a short between it's output and ground.
If output is shorted to ground, check the solder joint on the 7805 input, big brown cap, and 1N4004 diode. Touch up as needed.
If the output isn't shorted to ground, you're drawing too much power through the 7805, follow the 7805 troubleshooting advice above.
You have a short between 5V and ground, look at the short to ground page.
You're sinking too much current on the VSS or Injector lines. Check the soldering on the 100K resistors. Measure the resistance on the 100K resistors. Unless you've hooked up several thousand volts, input voltage is unlikely to be a problem.
Make sure the VSS and Injector inputs are below 100 volts. If they're over 100 volts, something is usually wrong anyway.