Some of this is easily possible, like monsters re-spawning, and the teleportation wall.
However, exchanging points into weapons and even items? Every player should have a value of how many points they have, which shouldn't be very hard via coding? But in mapping, that's probably impossible.
Now, gathering minerals should also require a new entity/ new entities (mineral_salt, mineral_sugar etc.).
But overall, this is a GOOD idea =D
Imagine traveling to Xen, beating the poop out of Big Momma, and then going to another planet, infested with other aliens. Did you mention cooking headcrabs?
Well, the idea revolves around space travel, and then you would also need new NPCs if you want it to be fun. Coding the NPCs could be simply copying the zombie code, or perhaps any NPC's code, or you could add new NPCs almost from scratch.
Then, you should need new weapons, like plasma guns etc.
But, keep all that in mind for the Episode 2. For the first version of the mod, I suggest finishing it without new NPCs and weapons.