OK, so hopefully missing something obvious here. I’m working on getting ideas across from the Isla to Ableton to develop the songs. I want to bounce the stems through my SSL SIX. So I just bounced them individually using solo over the master out and into mono tracks on Ableton. There is latency as I expected, so I thought to fix that I could just look at the kick, snip out the latency and pull everything back by the same amount. That did not work. It looks like they all recorded with different amounts of latency. 
I’m using a UAD Apollo 8. Can anyone suggest what I’m doing wrong, or tell me how you do it? Thanks.
Not doing anything wrong and this is expected if I’m reading your post correctly. As I understand you are muting and or soloing individual tracks on the 2400 and then recording them into Live. Unfortunately most daw clocks have jitter that is quite different between takes- even with sync. This happens with every outboard box I’ve owned. So the good news is it’s nothing wrong with the 2400. Now… what to do about it?
- record the individual outs either over usb or through the 6 all at the same time. Then you would just need to snip off one amount of latency as all of the tracks will have been seeing the same amount of drift at the same time.
- continue as you were and just know that you may have to do a bit more detailed editing to line it up.
- don’t worry about the few ms differences unless they are audibly changing The results
- hire an engineer so you don’t have to do the detail work. Jk
- some folks try external clock sources but I can’t speak on their effectiveness
Thx thought it might be jitter. Had a nightmare with my TR8s for that reason too. Want to go through the six as it adds really nicely to the sound so don’t want to usb. Can’t do them all together as the six doesn’t work like that. I don’t have an issue with editing the files, but when there isn’t a note on the first beat of the bar it’s a little abstract, especially with heavy swing on some of the parts. It really does mess up the sound. Thinking out loud I wonder if the answer it to run for a few bars and take from later bars when jitter will have ironed itself out, sure I’ve seen people say to do this. 
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Worth a try but I don’t think it will. If you sync the 2400 to any DAW you will see the jitter in the tempo meter. I use Live primary but have seen it in Logic and Cubase as well.
My trick for this is very lo fi (and works for any gear, effects, etc)
- Find a sound that has a very clear starting point (zero crossing is super obvious)
- Create a new 8 bar pattern with just the sound on the 1 of every bar for the first 4 bars (let’s call this pattern “roll in”)
- Same - but with the sound on the 1 of every bar of the last 4 bars (call this one “roll out”)
Now…
- When you record, start with roll in - so you record your sound. Switch to what you actually want to record, then record roll out
- Repeat for all stems
- In your DAW line up all your stems so that the sound helps you get perfect visual alignment
- You shouldn’t need to - but from here align by ear
The unofficial name for this is pmpte (pronounced pimp-ty) as I’m rhymes with smpte because it’s the diy version of it
No particular problem here when leaving 2 or 4 bars blank at the beginning and syncing with MIDI.
Recording multiple takes is fine as well.
Like first time with no filter on the melodic samples. Second time analog filter. Third time digital filter.
What about have the metronome pre-roll before your track plays?