So I went to 4 pet shops yesterday and I'm feeling overwhelmed... so many options, and it just seems like all but one place (this was the most expensive by far, of course) may not know what they were talking about! I think they just don't care as long as they sell something!
Unfortunately this is the case with some LFS's. Once you do a little reasearch on your own and ask some questions here you will get a better idea of the shops you want to do business with.
1 -I'm no closer to deciding between the tank choices.
Understood. I can tell you that I started with an all-in-one (AIO) tank and I loved the simplicity of it and am glad I started there. I now have a "component" tank that I like a lot as well and have a lot more flexibility. Go as big as your space and wallet will allow. Yes the tank will be more stable but just like in FW you always want something bigger. If you are serious about keeping a healthy tank you can do a small tank.
Of course the benefit of a component system is being able to select exactly what you want for everything from lighting to flow to filtration. They are also a little easier to add a sump to (especially if you get a drilled tank) if you go that route.
Bottom line is that people have a lot of success with both setups. Go with what you like.
2 -I'm completely confused about the lighting differences between compact fluorescents and t5 lighting. Am I understanding that the t5's are lower watt yet higher output?
The biocubes are outfitted with PC lighting which will do fine for most/all soft corals (mushrooms, etc.) and a lot of LPS (large polyp stoney) corals but will not suffice for most/all SPS (small poly stoney) corals. Take a look at some of the SPS corals (acropora, montipora, etc.) and decide if you are going to want to keep these. If not, I think the biocube will suit you fine. This is just my opinion but if I was not going to get a cube, I would not buy a PC light fixture and stick with T5's, halides or LEDs (or a combo fixture). PC lighting is fairly limited when it comes to color and spectrum selection. You can usually only choose between a daylight bulb, an actinic (blue) bulb or a 50/50 bulb which provides one daylight and one actinic. In a T5 fixture you have a lot more choices especially if you opt for a 4 or 6 bulb fixture. I am fairly certain that you can buy custom hood for cubes from places like nanotuners.com that have been retrofitted with halides, T5's or LEDs (maybe even a combo of these) that would open up your coral choices. I suppose you could also find a cube without a hood and get your own light such as a pendant style or clip on halide such as a K-2 Viper or if your handy you could build your own fixture.
3- Live rock. The best looking rock that I saw was beautiful, but also $11.99/lb, Some moldy brown looking for about $5/lb.
4 - Base Rock, way cheaper...and some really nice structures. Can this be mixed with the nicer rock to save some money? If so much then to what ratio?
Buy the best rock you can buy BUT you can buy a few pieces of the quality stuff and use it to bring the base rock (assume you mean dry rock) to life to save you some money. 50/50 split will be fine and you could even go with a little less live rock. It wil take a little longer to cycle this way but it will save some $$$. When buying LR ask about how long it has been curing and look for things like coraline algae growth and critters crawling all over it. This won't tell you everything about the rock but its a step in the right direction.