A few simple "find/replace" commands in MS Word will add most of those code commands when you've finished your work on it. That conversion between the first example and the second one wouldn't be a problem.
For example, if you started with the original text
Mat 1:1 The book G976 of the generation G1078 of Jesus G2424 Christ G5547, the son G5207 of David G1138, the son G5207 of Abraham G11.
You could do a find (with wildcards on, and without the quotation marks) "^13(Mat [0-9]{1,2}\ ([0-9]{1,2}) "
And replace it (again without quotation marks) with "^p<SV\2>"
And you would end up with
<SV1>The book G976 of the generation G1078 of Jesus G2424 Christ G5547, the son G5207 of David G1138, the son G5207 of Abraham G11.
The book and chapter specific codes would have to be entered manually, but that's not that difficult.
Now, regarding the interlinear, that's another can of worms all together.
I don't know if you can create a macro that inserts stuff into different cells of a table. If so, then getting the references in a separate column wouldn't be that difficult. But that's beyond my area of knowledge.
Edited by Bradley S. Cobb, 15 February 2013 - 02:34 PM.