Ok so here's the situation.

Started with two light sockets in my garage ceiling, wanted to replace them with outlets so that I could hang four flourescents. Didn't note the original wiring, now I'm tearing my hair out.

Garage has two boxes in the ceiling, and two 3-way switches

Switch A has two bundles of wires (Untouched and presumably still wired properly)
Bundle 1: White + Black
Bundle 2: White + Black + Red

Box A has three bundles of wires
Bundle 1: White + Black (this black is always hot I has discovered)
Bundle 2: White + Black + Red
Bundle 3: White+ Black

Box B has two bundles
Bundle 1: White + Black + Red
Bundle 2: White + Black

Switch B has one bundle (untouched and wired properly)
Bundle 1: White Black Red

All of this is somehow connected to my front hall, the front hall has 3 three way switches, a light, and an outlet.

An Ideas?

In order to help you I need you to think about what you are saying with the term "Outlet"

An "Outlet" means the hole in the ceiling with the wires running into the ceiling box. Is that what you mean by "Outlet", Or do you mean that you wanted to put "Receptacles" into the "Outlet"?

One thing to consider is that if you live in an area that gets very cold, is the Fluorescent lights are slow starters in cold weather.

To your wiring question. The most critical thing I need to know at this point is to determine where the power supply cable is. This should be a black/white/bare ground cable. Black is the hot conductor. White is the Neutral (Return) conductor and bare is the grounding conductor.

A three way switch does not use neutral, in fact only specialty switches and current level (2011 NEC ) require the neutral at a switch outlet.

Normally, I would expect to find the Black from the switch connected to the black from the power supply. At the switch, Black should be connected to the darker of the three screws.

The lighter colored screws provide connection for the "Travelers". These will be the Red and White conductors. The white conductor should have a band of red tape around it to mark this conductor as a hot conductor.

At the other switch, again the travelers connect to the lighter conductors. Black connects to the common post. The other end of the black connect to the feed for each light. Both whites from the lights connect to the white from the supply conductors and of course the bare grounds connect to their respective posts.

This is not going to be easy.

Describe the wiring connections at switch A. Do not disturb, just describe them. Which wires are connected together and which wires are connected to the switch. Also tell us which wire is connected to the common terminal of switch B.

The correct terminology for the way you use bundle is cable.

Also tell us something about the environment, is this wiring something that could have been done by a non-electrician?