I'm running track drops with a Nitto Pearl 9 (which in actuality is around 98mm/100mm). But I'm not satisfied with it because I have a short head tube and it's preventing my stem from going all the way down thus making the stem protrude too much.

If I were to swap out the pearl for a jaguar, what size would I need to get to compensate for the drop? I'm trying to keep the reach relatively the same and I usually only ride on the top of the bars. Should I go shorter and get an 80mm jag or stick with a 90mm?

I'd been in this situation before. This is going to sound like overkill but it's what I've done. Leave your current stem on the bike how it is.

1. Get the dimensions (length and angle) of the new stem you're considering.
2. Grab some cardboard or other stiff paper.
3. Draw a straight line (this will represent the part that goes in the steerer).
4. Draw another line starting at the top of the first line, extending for the length of the stem, and at the appropriate angle.

Hold up the cardboard behind your other stem.

Woolah! Now you can more easily figure things out. E.g., you can easily tell that it'll be further out, closer in, lower, higher, etc. And you can also figure out the proper length to keep the same reach but lower.

TLDR: Draw it on paper.