Your signals look extremely well time-aligned (within a sample).
Since you have NaN, I suppose you could just perform a weighted comparison over the points you currently have. Maybe something like:
function D = mdist(X)
n = size(X,2);
D = zeros(n);
for i=1:n
for j=i+1:n
idx = isfinite(X(:,i))&isfinite(X(:,j));
D(i,j) = rms(X(idx,i)-X(idx,j));
end
end
D = D+D';
>> mdist(subset)
ans =
0 0.0002 0.0005 0.0009 0.0015 0.0022 0.0030 0.0039 0.0049 0.0059
0.0002 0 0.0003 0.0008 0.0013 0.0021 0.0029 0.0038 0.0047 0.0058
0.0005 0.0003 0 0.0005 0.0010 0.0018 0.0026 0.0035 0.0044 0.0055
0.0009 0.0008 0.0005 0 0.0006 0.0013 0.0021 0.0030 0.0040 0.0051
0.0015 0.0013 0.0010 0.0006 0 0.0007 0.0015 0.0024 0.0034 0.0045
0.0022 0.0021 0.0018 0.0013 0.0007 0 0.0008 0.0017 0.0027 0.0038
0.0030 0.0029 0.0026 0.0021 0.0015 0.0008 0 0.0009 0.0019 0.0030
0.0039 0.0038 0.0035 0.0030 0.0024 0.0017 0.0009 0 0.0010 0.0021
0.0049 0.0047 0.0044 0.0040 0.0034 0.0027 0.0019 0.0010 0 0.0011
0.0059 0.0058 0.0055 0.0051 0.0045 0.0038 0.0030 0.0021 0.0011 0
