FCP crashing after 999 sequences in a project

The question is... do you have 999 sequences in your project?

Let's make sure we are using the same terminology here.

A Sequence in Final Cut Pro is basically a set of clips that you have chosen and placed on the Timeline.
If you have somehow managed to have 999 Sequences open at the same time, then the mind boggles!

Or are you referring to 999 individual clips (edit events) in one Timeline Sequence?
That should be no problem at all. You might be thinking of some ancient EDL format which certainly has limitations.

What is the file size of the project?

Whoa dude! That's like three times bigger than a project should be. Generally when you hit the 50-75MB mark you should think about breaking it up. If you're doing commercials over a long period break the project up into time chunks.

Yes.