I just picked up an old military CJ5 with a straight 6 and a 4wd
transmission.

It seems it has been modified a little, and by checking the serial
number near the firewall I found out that it isn't a standard type,
but has a "C" for Custom.

Here are the symptoms.

It idles fine, however, when in gear with no gas, it has a lot of
small pops/backfires out of the exhaust pipes. A word about the
exhaust: after looking under the carriage, I saw that it had what
*could* be a custom job. The exhaust pop runs under the drivers side
and a muffler is mounted there. The catch is, another pipe is run the
same way, with a muffler, under the passangers side, connected to the
side of the pipe which goes to the drivers side. Because it moves in
the path of where the drive shaft would go to the front differential,
that was removed, so in 4wd the transmission is just sort of spinning
and not turning the wheels.

The other symptom is, with very little gas, almost barely enough to
register, it sputters like a car would sound when it is running out of
gas. With the peddle depressed enough such that it is getting a fair
amount of throttle, there are no problems, other than it is very loud,
but that's not really a problem with me ;)

What could be causing this? Some observations I made that may be of
no consequence:

There is what seems to be an insulating piece roughly 1/2 an inch and
tan in color between the intake and the carb (I'm new to anything
mechanical with cars, so bear with me). When I moved the throttle
with my finger on the carb, it slightly saturated with gasoline (i'm
assuming what this is) and turned a darker shade. This didn't seem
right to me! Perhaps this is a problem.

Vacuum problem occurred, but again I'm very new to cars in general so
I don't know how to check on this, and just turning random bolts on
the exhaust manifold didn't seem like a good way to getting to work
every morning.

It has had new plugs put in (gap problem?) a new control unit (small
box, not sure how much this controls these older jeeps vs. modern
computers), a new distributor it looks like, and a new oil filter from
what I can see (the new vs. old parts stick out like soar thumbs - ie.
rust vs. shiny plastic.) oh yeah, a new battery as well.

I'm sort of at a loss, because I'm very new to fixing cars, but I'm
intensely interested. I just started reading up on them a few days
ago, after not knowing a tie rod from a piston.

Thanks in advance :)