Hope this isn’t a dumb question but do I remove the foam under the tube and the tape on top of the tube before I fire up the machine?
You can. Won’t hurt anything being there.
Yeah don’t leave the foam in there. It’s just for packing purposes & I recall the paperwork that came with mine said remove it. Not sure about tape on top of tube. Most tubes have a sticker on them with some sort of tube specs which is safe to leave on it.
Another question is water only suppose to flow thru the inner tube? I have no water in between the smaller tube and the outer tube
Correct. Water in the water jacket only. Make sure there are no air bubbles. None.
@Gee_Willikers good to know… I have rotated the tube while the pump is running and all other electronics off to purge all air bubbles I will let the pump run for 24 hours to purge any entrapped micro bubbles
First matter of business tomorrow after work… Cut some sharks… With a fricken laser beam 
Can someone tell me what the purpose of the coiled pirex tube is?
Google says gas return tube. I’m assuming its coiled for added length/longer gas cooling time.
Sharks with lasers. Nice.
A point to remember for the water flow is to place your water tank higher than the tube, that way gravity assists in keeping bubbles out of the tube when you have the pump turned off.
Since you’ve moved the tube itself, expect the alignment to be off.
@Alex_Krause Gee Willikers is correct, if you have been “rotating the tube”, you will need to do a full mirror alignment. Read all the information on doing it first. Yuusuf posted a great paper on how to do it. It can takes hours to get it just right so do not get discouraged.
@HalfNormal I did? I don’t recall posting much about mirror alignment. Maybe I post too much that I don’t even remember.
But, there is a great guide for mirror alignment floating around here somewhere on the main page. I believe it is stickied up the top.
@Yuusuf_Sallahuddin_Y you are correct. It was @Scott_Marshall . My mistake.
I also had to move my tube away from the lens several mm in order to get everything to focus properly.