I have done the Weber conv. a while back and since then it seems that my brakes feel spongy. After a brake job and bleeding multiple times they still aren't braking like they should. I'm just trying to figure out if maybe a vacuum line or something I threw away in all that mess could have had something to do with it, or is it just my booster going bad?

Your Brake Booster Vac Line maybe leaking.
Also I believe they are Metric diameters, so get the right size if you replace it.
In my "Minds Eye" i think it vac line connects to a metal tube which crosses over to the passenger side
and then hooks to the intake via another rubber vac line.
And last, bleed your brakes, longest BACK brake line first, next back brake, longest front, last front.
Also available are these niffty "Auto Bleeders" that replace your wheel cylinder/piston bleeder bolt!!
You crack them open like normal, they have a check valve inside, and you can bleed them my yourself,
tighten them when all air is out, and your done.

CAPT

Just an FYI if it is an early samurai the brakes are in a X configuration, right front left rear, same front line from master, left front right rear same line kinda thing if it's driving you crazy Lol.

I have done the Weber conv. a while back and since then it seems that my brakes feel spongy.

Define "spongy".  To me it describes a situation where stepping on the brake pedal give you the sensation you stepped on a sponge.

There's no real connection between the carb and the brakes, other than the booster, and a failed booster or disconnected vacuum line would/should not cause the brakes to feel spongy - they would/should feel hard or unresponsive because of the lack of power assist.  Spongy brakes are usually caused by air in the lines compressing and giving the added "spring".

Switch off the engine and step on the brake pedal a few times (to bleed off any stored vacuum), by the third or fourth time the pedal should be "high & hard" (near the top of it's travel and moving a small distance) - if it's not, you have a brake system problem.  Next, whilst maintaing pressure on the brake pedal, start the engine - as the engine starts the brake pedal should drop an inch or so - if it doesn't you may have a booster problem or a disconnected vaccum line.