So I was doing a bunch of quests yesterday and was getting ready to buy all the mats I need for the Red Rebel trade from lvl 3 Jaeger when, much to my dismay, I realized that doing "BP Depot" for Prapor had brought me back down to lvl 2 and I'd have to finish Tarkov Shooter pt 1 (mosin scav kills w/ iron sights, yuck)
Talking with my homie I realized he had finished "Shady Business" which gives you +.04 Jaeger rep but for some reason I didn't have that quest available. The only requirement listed in the Wiki is being lvl 20, and I'm lvl 24. I couldn't figure it out, got butthurt and logged off last night but today we figured out that that it wasn't showing because "What's on the Flash Drives" is a pre-requisite quest for "Shady Business" and I'm happily working on Flash Drives in my hideout.
TLDR: If you need Jaeger at lvl 3 and you don't want to do Tarkov Shooter: don't worry about losing rep with Jaeger for the Skiier and Prapor quests, you'll make it back from "Shady Business," which gets unlocked w/ Jaeger when you turn in the skiier quest.