ltspice matlab optimization
Here is some code to run a sim from matlab. One option would be to generate a netlist file from the .asc and run that from the command prompt, you could even change the netlist file from matlab and add, delete components or in the least change values. 

Another idea I've had is you could also do this with netlists and write the netlists from matlab and even do genetic optimization with circuits by having matlab write the circuit for you, then run the circuit, then check the result in matlab. 

Anyway here is the code, I changed some names and you don't have the .asc files or the write nets, so the code will need some retooling but here is an example of how to get the code out. 

You'll also need the function Ltspice2Matlab within the scope of this code.
An advantage is I don't think the function generates Nan's and has a good timebase that it returns. If it does you can simply replace the Nan's with the previous value or and average of the previous value and the next value using isnan

status1 = system('C:\...\LTspiceIV\scad3.exe -Run -b blah.asc')

comparerun = LTspice2Matlab('blah.raw');

status2 = system('C:\...\LTspiceIV\scad3.exe -Run -b blah2.asc')

comparerun2 = LTspice2Matlab('blah2.raw');

%get some data from netlists out of the raw file
cVres = comparerun.variable_mat(find(strcmp(comparerun.variable_name_list,'V(one)')),:); 
cVzerostage = comparerun.variable_mat(find(strcmp(comparerun.variable_name_list,'V(two)')),:);
cVthree= comparerun.variable_mat(find(strcmp(comparerun.variable_name_list,'V(three)')),:);


% figure;plot(baserun.time_vect,Vthree)


ylabt = 'Voltage';
tittx = 'title goes here';
h = figure;subplot(20,1,1:12),plot(Vres,cVthree),hold on,plot(cVres,cVthree,'r')
legend('Origonal Run','Compare Run');
title(tittx);
xlabel('xlabel')
ylabel(ylabt);

% if you want to compare the two runs with a residual
interpV4thstage = interp1(comparerun.time_vect,cVthree,baserun.time_vect);
subplot(20,1,17:20),plot(Vres,Vthree-interpV4thstage,'m')
title('Residual');
xlabel('xlabel')
ylabel(ylabt);