The pulldown would ensure it doesn't start on while the outputs are high impedance, once they are set as outputs and either high or low it doesn't matter, you could probably get away without them but thereon almost always therehow much draw on the 5v line are you using? Dropping ffrom 12v to 5v is basically wasting more than half the power as heat with a linear regulator
How about one of these little assemblies for 12V to 5v conversion?http://www.digikey.com/product-detail/en/OKI-78SR-5%2F1.5-W36-C/811-2196-5-ND/225978
Something I noticed was the traces coming off the row of transistors up the top. If the through hole pads are on both sides, the trace from the middle pad gets VERY close to the right pad on some of them. Some of the other clearances look a bit tight too.You can set up EAGLE to run DRC to check for minimum clearances etc, might be worth checking the specs of the fab house you're going to use and check your layout with those values. Good luck!