Yes, that's a good question - why exactly are you trying to recompile Half-Life?
If you intend to mod it, you may be able to find a modder community that has a cleaner base code that will compile easier. Think something like ioquake3, just for Half-Life instead.
If you're trying to just tinker with the source code and teach yourself how to program, then a much better bet would be to find a cleaner base code that's more updated. Excellent examples would be Half-Life 2, pulled directly from Valve through Steam, or, again, something like ioquake3. I was able to compile ioquake3 with absolutely zero work - I just downloaded it, opened it, and compiled it.
Really, I don't know how beneficial it is to try and clean up crusty old code. Beginners will learn much more by getting involved in the mod community. Experts would probably pull out their old Windows 98 machine, boot up VS6 and go from there ;-)