Here are my thoughts on some of your questions:
RODI Unit:
Using RODI water is an absolute must in this hobby. I most definitely would not trust well water to be used directly into my tank. Besides just the common contaminants, there is the potential for several others that you just don't want to introduce into your tank. Now, you have two options to get that water.
1. Buy it and lug it from the LFS. This is what I have been doing for the past 13 years of being in this hobby! I was forced to do it largely due to space limitations that would not let me install an RODI unit. I do have the space now, as well as a unit so installing that is my next project.
2. Install your own unit and have water at your disposal in house.
BRS makes a great RODI system. I got their 6-stage water saver system. (
http://www.bulkreefsupply.com/brs-6-stage-universal-water-saver-plus-ro-di-system-150gpd.html). The price difference bettween the 75gpd and 150gpd systems wasn't that much so I decided to get the biggest one available since it will make the water twice as fast. BRS is having a 10% sale today so if you're ready to get one, today might be a good time
Protein Skimmer:
This is where you will see the biggest price variances. I am on a budget so after doing lots of research, I found several people who have had good things to say about the SC Aquariums skimmers. They are very reasonable, and do a great job. I have the SCA-301 model and it pulls out some nasty gunk. You will need the SCA-302 for your size tank. (
https://www.amazon.com/SC-Aquariums...F8&qid=1467649460&sr=8-3&keywords=sca+skimmer).
Lights:
I have recently switched from T5s to LED. Again, budget limitations have kept me away from the fancier ones like Radions or Kessils. Once again, after talking to several people, I found a fixture that people have been very happy with, and have shown to give good results. They are the Ocean Revive fixtures. I have two on my 40 gallon tank and could not be happier! They may not provide you with all the bells and whistles like sunrise, sunset, ramping up, wifi/bluetooth controls etc... but they are a solid fixture for a fraction of the price. Aquatic Marine sells them for ~$180 a piece. You will need two of them as well. Not sure how much your current fixture was, or what your budgetary constraints are, but I would highly recommend you go with these lights instead. Here is the product from the Amazon website:
https://www.amazon.com/OceanRevive®-Arctic-T247-Spectrum-Dimmable-Aquarium/dp/B00YOYD3K2/ref=sr_1_1?ie=UTF8&qid=1467649784&sr=8-1&keywords=ocean+revive+t247
You can check out my build thread to see what they look like on my tank.
Let us know if you have any other questions, or need any more specifics on the above.
Cheers!
Yash