first off, gl on the mod, im currently trying to figure the in/outs of moding, ive gottin most of the menuscreen GUI modded, im currently looking for a list of files needed/ possible to mod, i have found some interesting things, i would suggest getting the latest version of the SDK(standard development kit) that helped me figure out alot of the files editable for modding.
as for your direct questions:
(1) i know that Wally (can be found on this site) its a texture editor, and doubles as a .pak file generator, however im not sure how you tell HL to use your pak file and not HL's pak file, or if you even need to, i did however notice that none of the mods (retail: BlueShift included) have pak files, i know not why that is, maybe they got lazy
(2) i believe the sound is withing there logo.avi file (name of avi file not sure) would be the simplest way of doing that. not sure if this is the method valve took though.
[addsig]