Can you change the cost or set some to inactive using LUA or an ini setting?
Basically, what I want to do is make some things very costly and others completely unpurchasable for one specific mission.... The current list of purchasable items is broad and the majority of items are fairly cheap.... I don't want to change this for the whole game, just one scene I am working on.

Any pointers/ideas?

you can use Lua to remove gold...

I don't necessarily want to remove gold.... The scene I'm working on sticks to the main theme of gathering gold.
Perhaps, instead of using gold as it is in the game, I made some objects that served as gold....
The small amount of gold you get in the map isn't necessarily the target you are supposed to go for, but it helps you just enough for you to get the gold bars/nuggets/etc throughout the rest of the map....

I don't really want to do it this way, it seems like the Fallout 3 way of modding, being forced along a certain path in order to create a mod. One of the main reasons I only made three or four Fallout 3 mods.... One, I felt was a really cool idea, but, without a complete revamp of the mod-creation process, I couldn't finish it.
I called it the rad-slinger; it fired a stew of irradiated matter that was supposed to only do rad damage, so it would be pretty much useless on bots and irradiated creatures, but would be fairly powerful against humans. The way I ended up having to get it to do anything was set the damage to the lowest setting, crit damage to lowest setting, and crit chance to the highest setting (So they would melt:D ), then add an explosion that only did rad damage. Then, I tried to add rads over time, like the mini-nuke, but that turned off all other damage including rad damage from the explosion.
Did you guys know that all NPCs in Fallout 3 are immune to rads? I turned on god mode and sat there for about five minutes spraying an NPC with the rad gun when it was screwed up and would only do aoe rads (set to almost insta-kill levels for the PC).... All the NPC did was say things like "Hey, watch it!"
I think that was really when I decided I was done. Effects that only hurt the PC when NPCs are identical in everything but looks and specific stats kind of ruined the game for me.
Sorry about the tangential rant there....

I was about to facepalm but I read the bit about specific mission.

Not possible to do directly. You could fake a buy menu (sorta) but that'd be ridiculously complicated and wouldn't handle different screen resolutions well.

I'm no Lua god, in fact I don't know anything about Lua (Except that people are divided about its pronunciation), but couldn't he make some script that changes all HDFirearms' 'Buyable' variables set to 0, and then the ones he wants active set to 1, and change it back when the script deactivates?

No.

And add gold.