Thanks for the help! My problem was sort of difficult and while I didn't use your suggestion in that explicit manner it did point me in the right direction. I ended up being able to figure this out with a combination of indexing and looping as you can see below. The difference between the netcfq array I referred to in the original question and the cfq variable referenced below is that row 1 in cfq is the initial cash outlay (a negative number) while netcfq are the cash inflows. The IRR calculation won't work with zeros or extremely small numbers as I found out by setting netcfq(netcfq<0) = 1/10^9 and then using the IRR function.
Thanks again!
Code:
warning('off','finance:irr:multipleIRR')
%IRR Calculations
irr_index_nz = sum(netcfq>0)+1; % row subscript of last day of non-zero cash flow
irr_value = zeros(1,size(cfq,2));
for i = 1:size(cfq,2)
rows = 1:irr_index_nz(i);
column = (i);
irr_value(i) = irr(cfq(rows, column))*12;
end