Tools for data organising and processing
I would store data in CSV (i.e. text file with a table, with values separated by commas) rather than XLS files (the first is easier to import from and export to anything). Otherwise many tools will do the job (if you are familiar with MATLAB - why not using it)?

For general data processing and manipulation, Python (with SciPy stack) is capable of everything you mentioned. In particular IPython Notebook is great for data exploration and presentation (you can use code, comments and LaTeX in such notebook - also for reports). For tabular data, use Pandas (R-like DataFrames).

For reports also you can create files in Markdown (with LaTeX), and then convert them to pdf with Pandoc - may be much easier than generation of LaTeX code. (To get you some taste what is Markdown - look at StackEdit.)

And alternative to Python is R, with knitr for report generation. If you are not sure, if to choose R or Python, then for your task R seems to be an easier and better way to start (especially with RStudio as an interface).

For a bigger list and links to tutorials, take a look at a list of software for scientists.