You may want too look into a thing called a Tank Circuit. It eliminates the disadvantages you have listed, and does everything your startup controller does. What you built seems very similiar to a tank.
I have posted a really bad component drawing of the one that I am using. Just to let you know, the +5v coming out of the PSU, through the relay hooked to the +12v Ignition line, and back into pin 8 on the COM port is for your shutdown controller. You setup a generic UPS in XP, so that when that pin looses power, it waits a specified amount of time, and initiates a shutdown procedure.
Personally, I have mine hooked up to a second battery thats hooked up to the alternator using a multiple battery isolator. This allows the system to hold on through crank. The battery was picked up for free at a wheelchair store. (it is one of the used electric wheelchair batteries. They will give them away for free since it costs them $$ to dispose of them. Just take a meter with you to see which ones still have a charge)
As you can see, there are two +12v lines holding open the other relay. This is so when you shut off your car, the relay stayes open, until the PC shuts off. As soon as that happens it will cut any contact from the inverter to the battery.
I hope that some of this makes sense, as it is nearing 2am overe here, and im nice and tired You can search back and find tons of stuff on these, and there are a bunch of people who use them, so just ask if you have any questions.