Does anyone have any good tips, build orders, or strategies for the Nakalim? I really enjoy the faction, but have been struggling to find a good method to winning on them. The best I've found so far is starting off with earlier aggression, since you automatically have the first set of ships unlocked at the start, and just trying to take out the nearest factions. Then from there, building up my fleets to take out the remaining factions. The only issue is that, if I can't manage to get relics, I quickly lose steam and can get out-teched. 

Thanks!

Caveat: My comments only apply to single player (Endless AI).

If you are asking about how to remain relevant in science mid- to late-game, then I think that the best answer is science behemoths. The effective research you get from science behemoths far outstrips what you would get from any other sources (relics, bluecap mold, generating science from battles, giving systems to the Academy, etc...). Once you hit the maximum 90% research cost reduction, along with the thousands of science production from the behemoths themselves, then the Nakalim become like any other standard 4X faction: survive and build up during the early-mid game, and late game is trivial. But obviously you'll still need relics to get to behemoths.

As for early game—completing the first three chapters of the Nakalim quest is helpful for free relics and can be done in the first 20-30 turns on normal speed. There is a very good guide for the quest on Reddit here. For chapter 1, I suggest curiosities for obvious reasons. For chapter 2, cancel religious law on the same turn you assign the hero, so you can immediately complete the quest on the next turn. For chapter 3, you can increase manpower by completing colonies, so with a bit of tricky timing you can have colonies complete right after you finish chapter 2, thereby trivially finishing chapter 3. This should give you enough relics until you get science behemoths.

One other thing that I don't see mentioned elsewhere is that if you prefer to build up and play defensively early, then you can trivially defend yourself by buying mercenaries from the marketplace. You generate a lot of dust by exploring and selling resources, so you can instantly deploy medium-hull mercenary defence fleets on any planet you want. I don't know if this is optimal, since most Nakalim guides seem to prefer early aggression.

The first techs I go for are neural robotics (for production) and impactless sites (for access to mercenary market); then one or two techs until behemoths get unlocked, and then behemoths from there.

I pretty much never give systems to the Academy. Early game there are no systems close by, and later the relics and tithe income are meaningless.