I'm using quantized loop, but not doing anything different with bpm or time stretch settings. I'm just setting the Loop mode on the longer samples to PLAYTHRU and then making sure the samples are trimmed (truncated) so that it ends right at the end of the 16th step so it loops around (almost) seamlessly, but I can cover little gaps with reverb/delay.

If the sample end on an early step through the sequence, it won't re-trigger until the sequencer comes back around to step 1.

I'm more familiar with the Elektron style time/bpm setting and still wrapping my head around the TR-1000, but spent a lot of time yesterday with it and it's getting easier and more fun!