As per the usual caveat, it would be far simpler for somebody to provide specific code solutions if had some actual data to work with rather than just descriptions; it makes for being able to actually attack the real problem. While the original files may, indeed, be large, the sample datasets don't have to be large at all other than that they are representative of the issues involved.
One comment on the code and remark...
typeA=T(T.var1='somerthing specific',:);
typeB=T(T.var1='somethign different' | T.var2='something else',:);
typeC=T(T.var1='somethign even different' & T.var4='something new again',:);
"I have lots of these already written out and they don't seem to lend themselves to automation."
Well, yes and no...selection of groups by one or a number of criteria can at least be made into generic code where what changes is the data. That can include the variables used in the comparison as well as in the values against which to compare. That alone can make a large difference in code compactness and maintainability--instead of having a zillion specific lines and sequentially-named variables, you've got a function or two to write/debug and then just data sets to create and iterate over.
Then, depending upon where you're headed, you might avoid ever creating the above new tables explicitly but only use the logical addressing vectors from them to select the subsets of interest dynamically and consume them in the output phase before going on to the next.
That kind of code structure is where need more details in order to be able to recommend better solutions.
As for the last about the variable names within a table -- those can be handled dynamically, just not by manual creation but by using some logic and patterns in generating them programmatically. Again, you may need to create some data arrays or you may be able to create/use base names from external input files, but there are clean ways to use dynamic names in addressing variables in tables and/or structs -- what you do NOT want to do is to create base variable names in the workspace-"there be dragons".
