So it goes. You can sometimes simplify things a bit, though. You might go ahead and apply your stroke, then go through and click on the masks one at a time to find where they are, and see if you can go without some of them. Many of them will be tiny, one- or two-point things that really aren’t even serving any purpose for what you’re doing.
Also, if you’re trying to make it all draw as one object – sort of an Etch-a-sketch effect – you’re probably (unfortunately) going to have to do a lot of manual masking – possibly simply connecting them so they all flow together.
Telling your Stroke to do all masks sequentially MAY work… but you’re probably going to have to go through your hundred of so masks and re-arrange them to make sure they’re in the correct order. Depending on what you’re doing, it may be easier to simply bring your original image into AE and trace it in one long, continuous mask.
Hope this helped a bit.