Wow, that's about as awful a GRE experience there can be... but at least you got to take the test and most of the drama came afterward. Makes me feel lucky that my computer and subject test centers were close by.
I had serious trouble writing my SOP, but I'd have to say the most annoying part is the recs since they're beyond our control both in terms of what they write and when(if) they submit them. Transcripts aren't a problem, as long as you send them early enough, since you can check to make sure they arrived before the deadline.
But no matter what I did, I knew some prof would wait until last minute. I'm quite lucky I was always down the hall from their offices so I could pop my head in once in a while, or otherwise it could have been worse... I can't imagine trying to get a rec from someone far away like an REU supervisor.
I had assumed at least that since Stanford's app was due Dec 11, 3 days before any of the others, that it would at least force them to get the rest in on time in case they were late with Stanford and I confronted them. Two of my profs sent all of theirs in before the 11th, but one of them did each individual rec last minute, which made me bite my nails through the whole process.
He actually had forgotten that Stanford was due the 11th (even though I had written all the info in a packet for him). If I hadn't reminded him he would'nt have done it. Instead of doing them all that day with Stanford's, he did each of them the day before their due date, except the last two, which were due on Jan 1st... I don't think he would've gotten those two in if I hadn't sent him a desperate e-mail the morning of the due date. He submitted those 3 hours before.