We present the design, and prototype phases of the intermediate frequency (IF) system for the upcoming balloon borne observatory, Galactic/Extragalactic Ultra-Long Duration Balloon (ULDB) Spectroscopic Terahertz Ob-servatory (GUSTO). GUSTO is a multi-organizational project whose goal is to address several key unanswered questions concerning all of the phases of the stellar life cycle within the Interstellar Medium (ISM). Using the NASA ULDB system for its platform, GUSTO will employ on-the-fly mapping techniques to scan a total of 124 square degrees of the Milky Way and Large Magellanic Cloud (LMC). GUSTO will survey the three brightest cooling lines in the Milky Way and the LMC. These lines are [CII], [OI], and [NII] corresponding to the three wavelengths of 158, 63, and 205 micron respectively. The completed survey will provide higher angular, and velocity resolution than that of previous surveys of [CII], [OI], and [NII]. These lines will be measured using three 8-pixel heterodyne arrays, each one dedicated to an individual cooling line, and all working together to make a 24-pixel focal plane. The GUSTO IF system is being designed to operate at low power consumption and high sensitivity all in a compact and lightweight package. The IF system will include a wideband 0.3-5 GHz, cryogenic, low noise amplifier (LNA), which will boost the IF output of a superconducting hot electron bolometer (HEB) mixer. The LNA was designed with commercial, off the shelf SiGe heterojunction bipolar transistors, and surface mount passive components. The LNA design has been optimized for low power consumption, and for sensitivity. The input impedance of the LNA is matched to the output impedance of the mixer over a wide range of frequencies to reduce reflections, and standing waves. Warm IF electronics have also been designed using commercial, off the shelf, surface mount SiGe transistors in order to achieve a high, and at gain (>50dB) over the entire bandwidth. These components provide variable gain and deliver an optimum signal level to the analog to digital converter of the backend spectrometer. The warm IF components were optimized for wide bandwidth, low power consumption, as well as reliability, and fit in a compact package. Commercially fabricated custom flexible printed circuit boards are being used for multi-channel stripline-based transmission lines, instead of the traditional stainless steel cryogenic semi-rigid coaxial cables. Replacing coaxial cables with the flexible printed circuit boards allows us to transmit through up to 16 lines on a single flex circuit, without losing performance, and furthering the design goal of providing a compact/lightweight solution. Each of the components used in this IF system will undergo rigorous qualification testing, and documentation in accordance with a NASA Class-D balloon mission. We discuss the design challenges in adapting cryogenic, and warm IF electronics to operate for an ultra long duration balloon mission.