So I gleefully finished the first mission, thinking that I would be able to go onto more missions and greater opportunities to utilize my hard earned cash, only to find that that was the end of the game. Quite a letdown.
Never figured out what all those rods, springs, glue and duct tape were for either.

Didn't realise it was that short, but I can answer the second part.
The random stuff is used to make weapon modifications, rod+spring i think makes for faster rate of fire or something.
There should also be some sort of metal tube and duct tape mod to extend your gun barrel.

Well that's why there's a map editor with the game so you can make it longer.
Or play the great mods for it like Sog69, Rubicon, Shady job,...

Always a good idea to check out the reviews at places like Metacritic. There are many highly-rated games at GoG, but Unfinished Business is not one of them.
You've done better than me, though - I uninstalled it after five tries at the first location. I got sick of having no chance to hit greater than 15%, and being hit by 70%+ of enemy shots from the same distance.

Personally I enjoyed JA2:UB, although it was rather short.
Nevertheless it's a nice game and there are mods for it enhancing the fun.
If you're new to the series, JA2:UB isn't the game to start with.
As for difficulty, yes it's harder than JA2.
Nevertheless you can choose the difficulty level.
When I played it first, I didn't have a JA2 savegame left, so I started from scratch.
Later on I imported my team from JA2.
In both cases the game was very playable, harder than JA2, but not too hard.
Duck and cover helps.