The main problem is there's limit to how fast you can issue commands. Between commands the instruments sit idle.
Try something along the lines of:
CONF:VOLT:DC 1V,0.0003
SAMP:COUN 1000
TRIG:COUN 1
TRIG:SOUR IMM
INIT
FETCH?
The INIT will start the sampling, and FETCH? will wait for the sampling to finish and return the data.
So you can set up your two instruments, send them both INIT, and then FETCH? the data from them.
If you need tighter synchronization, then you can have one instrument trigger off the other. Hook up the
trig out BNC on instrument A to ext trig in BNC on instrument B, then set instrument A to output a trigger:
OUTP:TRIG:SLOP POS
Then on instrument B have it trigger off this, instead of TRIG:SOURCE IMM use:
TRIG:SOUR EXT;SLOP POS
Then on B issue INIT, and on A issue INIT. A will start sampling and issue a trigger for B to also start.
Then FETCH? on the two instruments to get the results.
Or something along those lines.