if your cells are all of the same size, try using cell2mat (to convert your cell into array) and then reshape (to change the size from 60x30 to 30 x 60, assuming each half stimulus will have to be paired to the consecutive row)
You code contains errors, see if this helps (it would be useful to have your stimuli variable as well to troubleshoot
stimdata = cell(1,31);
for i= 1:2:size(stimuli,2)-1 % skip even numbers
if abs(i - size(stimuli,2)) >=2 % this should check if you have enough free stimuli to select two in a row
stimdata{i} = [stimuli{1,i},stimuli{1,i+1}]; % pair odd and even stimuli
cnt = cnt+2; % not sure why you want this one here
else
stimdata{i} = [stimuli{1,i}]; % pair odd and even stimuli
end
end
