I have just spotted your post. It has given me lots of problems, trying to remember what I did so long ago!
To answer your points:
"1. Where in the macro does it specify the number of columns at the beginning do not repeat?"
this is based on the first four columns being fixed data, the next 3 being Deposit/Time/Location so go to 8 to start copying
"2. Where in the macro does it specify the number of timepoints."
It does not. The procedure will repeat until there are no more timepoints.
"3. Where in the macro does it specify the number of columns per timepoint."
Having set up the start of the second column as 4 + 3 so next one 8 (as in 1 above) keep adding 3 until there is no more data (as in 2 above)
I hope that this explains things. I am now going offline for a couple of weeks, so anyone else please feel free to answer any follow up questions.