1998 Honda Civic DX Sedan - Timing marks not alligned.

[Lastofthebreed]

So, my daughter's 1998 Honda Civic DX, (135k) will only roughly start with the throttle floored. And even then you have to fight to keep it going. I'll start this by saying first and foremost that I am NOT a small engine car guy, and my mechanic experience is limited to old school engines, like pre-90x Chevy 350, 327, etc.

She drove it without issue from one place to another, then when she came back out to leave an hour later, no start/hard start. 

I did all the basic trouble shoots I could think of. Pulled the plugs, they looked fouled, so went ahead and replaced plugs and wires, verified spark with a tester...still no start. Verified fuel, and air. (Didn't do a fuel pressure test, yet, due to the following reason).

Here's where my question lies - I had the timing belt replaced 6 months ago, when we first got the car, just out of precaution. (I was actually very surprised, and pleased, to see how clean everything looked when I got a chance to see in the valve cover while the mechanic was working). Out of curiosity, while trouble shooting, I decided to pull the top timing belt cover off, JUST to make sure that wasn't at issue. Belt still looked just like new, not loose, no signs that it had slipped a tooth, etc. BUT...It just happened that the cam pulley was at TDC, but when I looked down at the crank pulley marks the TDC mark (far right white mark) was WAY (like 3 inches) to the right of the pointer marks. I haven't gone so far as to pull off the front wheel, and tear things down, to access the lower cover to check the drive pulley marks, but also can't for the life of me figure out how on earth the timing marks on the crank pulley could be so far off from TDC on the cam pulley, without the timing belt breaking, or at least tearing up a bit. All the pulleys are keyed, right? So there's no way it could have been put on in the wrong position. Why would the timing marks be off that way, and if that's the cause, what would make it happen so suddenly, while not even running?

Thoughts?