MMB automatically generates 'false-colour' (plain rgb) images for every filtercombination (L256/257/456/457/247/...) and spits them out in the 'gen' folders (opposed to 'raw' folders).
The images retrieved from Daniel Crotty's site are radiometrically calibrated images from which Daniel created approximate true color images (see 'Methods for Pancam Multispectral Color Imagery'
on his site for details).
You can create color images yourself through image processing software such as Adobe Photoshop, Corel PhotoPaint etc... by stacking for example L2/L3/L4 for red, L5 for green, L6/L7 for blue from top to bottom as layers and then adjusting the levels per layer by removing (0-255->output 0->0) green&blue for red, red&blue for green, red&green for the blue layer. By making the layers transparent you get color. From there you can manipulate further by using for example the channel mixer in PS as an adjustment layer or directly after merging the layers.
As for stitching manually or through some scripting, google for PTgui, Panorama Tools, PTassembler, Realviz, Autostitch, ....and see what you like best to start of with.
Also, search the forum for these as a lot has been discussed in depth and it will provide a lot of help.