I had my car up to replace my springs yesterday, and replaced the manual transmission fluid at the same time. I'm at 85k km and just figured it was time; according to my records neither of the previous owners had done it. I used Redline MTL, and drained it for several hours before filling it until it came out the fill hole. I ran about a third of a quart through before filling it.

Now at a certain point under hard acceleration, particularly in second and third gears and between about 2500 and 3500 rpm, I get a weird kind of vibration through the whole car. Any guesses as to what this could be from? It's too high a frequency to come from the spring swap I did at the same time (i.e., it doesn't feel suspension related). Does MTF take time to "break in"?

 

You changed springs to lower it, right? The axles need time to set w/ the new angle.

 

That's exactly what it feels like! Got it. So should I take it easy for a bit? How long will it take? What exactly happens as the axles set? Thanks!

 

Your axles already have wear patterns after running x miles on stock height. After lowering, you're suddenly changing the rotational & movement paths out their initial wear patterns, thus the vibration (usually at 1-2.5k rpm range on 2nd gear). Set duration would likely be dependent on many factors like miles ran, driving style, usage (track or street), etc. No1 can really tell.
Just make sure you do periodic checks on cv boots. Lowering on springs isn't known to be as damaging to axles as slamming them on coils. Depends how low you go. In case you blow your axles, best to replace em w/ OEM quality as cheap ones won't really stand the stresses of lowering. Just my $.02.