I've manually been following the Alliance Judgement guide from the Google docs and I'm currently level 32. Can I install Guidelime + the Judgement guide and it will automatically pick up my progress or how does that work?

Guidelime will automatically complete steps for quests you've already done. So shouldn't be a big problem to start even if you're 32. Most guides are split up into sections. From 10-20, 20-30, 1-6 etc, making it easier for you.

Yeah and if you continue with Judgements guide you will have no problem at all since you will already have done all the correct quests.