Alright here comes a super long post.
First off, spoon, thanks for the comments and advice about staying away from the clear tubing. We are going to stick with it for the time being and when the algae starts we will try replacing it over and over until we get tired of it. The hose is cheap (37 cents a foot) and we only need like 2 dollars worth every month or two if we switch it out regularly so that's not too bad. Also I might try black vinyl tubing instead of clear somewhere down the line, that should fix the light feeding algae problem. Our aim name is Conceyted, just like the name on here.
Alright now for the text and tank update... As you all can see we did our first wet run of the tank. We got the tank in Friday and over the weekend we spent our time finding bulkheads and talking to Nagel about what type of standpipe to build. We were very close of ditching the standpipe idea and getting the other tank drilled in the back middle and creating an overflow box inside of the tank. We decided to build the standpipe and once it was in we would make the final decision on whether or not to ditch the standpipe idea. Nagel suggested we build the standpipe he designed for his tanks. As you can see, we did.
Nagel's standpipe worked great. It does exactly what we need it to do! The only thing we need to do to complete the standpipe is the slip bulkhead screen. We actually went to a LFS today to get the 1" slip screen and Rick from Rick's Reef showed us some of his standpipes. He actually used some plastic mesh netting material as a grate in the standpipe. Not only did it quiet the funneling down the same way the bulkhead screen did, he also assured us that the mesh would be less susceptible to clogging. We will be going to lowe's tomorrow to look for the mesh but I couldn't find the stuff at home depot so I am not too optimistic.
Anyway, the standpipe ended up looking great, and once it is painted black and the black background is added to the tank I think everything will end up looking perfect. BTW I painted the PVC tonight using Krylon Fusion paint. Should come out great.
When we first assembled the tank you can see in the pictures we had the protein skimmer hanging on the back of the tank. Upon turning it on and hearing the loud cement mixer sound, we decided we were going to figure out a way to get that thing in the stand or we were only going to run it during the day. It ended up fitting great and it works absolutely perfect. The only problem I can see might arise would be the fact that it requires the sump to be 2/3-3/4 the way full for it to work. That means if evaporation takes out a gallon of water a week we will have to be topping it off fairly often to make sure the protein skimmer isn't running dry.
After that was settled we started playing with the reefkeeper aquarium controller to see all of the different settings we could do. Another problem arose! It seems we have too many things plugged in! The reefkeeper comes with a power outlet for 8 separate pieces of equipment. Well: 2 maxijet 600's, a return pump from the sump, the protein skimmer, the moonlights, the daylights, and the actinics make up 7 of the 8 outlets. Then the fan for the light needs an outlet but so does our heater for the aquarium, as well. Now we bought a Hydor Theo heater, and people are saying that they end up heating up much higher than they are set to, so our plan was to have the reefkeeper monitor the temp and turn off the heater at the temp we wanted it to be at. That way if the heater didn't turn itself off then the reefkeeper would. We don't have the light in yet, they ordered the wrong light so when we went to pick up the tank Friday we told them to just not charge us for the light and we ordered the one we wanted online. The light should be coming in tomorrow and we will find out if the fan is going to need its own outlet. We will keep you posted on the outlet dilemma!
So after these initial problems we started thinking we should write out a list of things we needed to fix before we got the tank up and running for real. Here is the list we made:
1) Fix leak in drain line from bulkhead
2) Find a solution to Bio Ball removal.
3) (and I just found this on the list!) Buy Jaime presents... HAHAHAHAH! my girlfriend is hilarious.
To fix the leak we will need to silicone the return line into the bulkhead so it creates a seal.
The bio balls problem might fix itself. As you can see in the pictures, at the beginning the water level in the sump was very low and the bio balls were not submerged. Therefore, with them removed it was creating a raining sound when the water was leaving the media tray and falling to the water in the sump. We put the bio balls back in to stop that noise for the time being. Once we moved the protein skimmer, though, we had to add more water to the wet dry to bring it up to operating levels for the protein skimmer. The bio balls ended up submerged and the sound of rain was gone so we are thinking that the water level being high will stop the sound and we can just put a bunch of rock in there for added bio filtration.
And to fix the final problem, well I think I will have to post a new thread in The Lounge section about that one, it could take me years to explain how I am going to fix that.

Thanks for reading guys, more updates to come!