I had changed my sleepmode in Terminal so as not to write the contents of the RAM to the Hard Drive when sleeping to save the 4 GB of disc space. I am not sure if this will effect what happens when the battery dies, but I am going to give it a shot.
I can't tell what changes you made in Terminal so there is no way to determine its effect. To eliminate all doubt I would drag the applicable preference file to the Trash.
When the Mac reboots, it opens all the windows that were open upon shutdown, but it takes a much longer time to reboot than it did when it simply resumed where I left off. Work doesn't typically get lost because Microsoft Word usually autosaves my work.
Starting a computer after shutdown always takes longer than wake from sleep since the OS has to be loaded before anything else can happen, and reopening all your previously opened windows always takes longer than otherwise since they have to be individually loaded also.
I would not be concerned about 4 GB of disk space; if its remaining capacity is so exiguous that 4 GB makes a difference, it's too full.
I am not sure what you're describing is abnormal.
My battery is definately in good shape. I always cycle it fully, and never unplug it mid-charge or plug it in at anything about 10% battery. iStat Nano says my battery is at 93% health.
Your battery is in good shape, but cycling it the way you have been is not the way to keep it so. There is no advantage to cycling it fully every time; that only worked with NiCd. Partial recharges and recharging at mid-cycle is OK with lithium ion and lithium polymer batteries.
It is best not to over-think battery charging any more. They need to be cycled but Apple's guidelines are but once a month. Each complete cycle reduces the battery's life; the amount of which is a function of its age, your usage habits, environmental factors and other intangibles.
