I just replaced the distributor on my '89 Civic and adjusted the timing.
After I did the timing, I got a little suspicious because the marks were funny-looking and yes, sure enough, I had carefully adjusted to match the mark on the timing belt cover up to a couple rust spots on the crank pulley.
I pulled the alternator belt to see better, and wrenched the crank pulley through several revolutions, but I couldn't find any real timing marks on that pulley **anywhere**. They are just gone.

Is there an alternate way to adjust the timing?

The thing is, the car actually drives just fine as is, and idles smoother than it used to. Is there a down side to just leaving it presumably wrong but running fine?

The crank pulley will have notches where the timing marks are, the paint probably wore of in the early 90's.

You would probably have better luck climbing up under the car and physically trying to locate the marks, then mark them will a colored marker or paint pen. Use a finger nail to locate the notches. Unless your pulley is completely beat up, they should still be there.

http://www.crxsi.com/repair/timing.belt/carank_mark.jpg

Wow, thanks for that picture, kris, that's perfect.
Those four notches are spaced exactly, precisely like my flecks of rust. I think it must have rusted in the notches.

No problem, glad it helped.