i would visually inspect your tubing after you drain.
Sometimes it will become very very cloudy. This has to do with the antifreeze and tubing.
If you want, you can retube it. If the cloudy tubes doesnt bother you that much, then forget about it, and just refill.
And yea, this is the one bad side about flushing your system. Your tubes get cloudy.
If you want to keep your coolant in your system for at least a year, i recomenda 1/10mix. It will last longer.
If your going for performance, and you dont mind flushing your system. 5% mix is be enough to give your pumps a slight lube, while maintain the max performance.
If you want raw performance, then use the distilled straight. However a flush every 2 months is usually required. Keeps the algae away!
The temp difference from top to bottom would be at most 3-4C so the choice is yours.
Honestly 3-4C isnt very much unless you load your cores 100% all the time, like F@H or WCG. And even then, its not a lot. But whatever makes you feel better.
Also, if you want to replace the tubing petras sells it:
Get masterkleer 7/16ID. Its just like that swiftech tubing you got with the kit, but clearer.
If you get the tygon make sure you get some worm driven clamps. Those nylon things wont work on tygon. Its too thick.
Lastly, if you really want to do a full maintence on it, you could take it all apart, and clean out your stuff.
To clean your block, you need to unscrew the top and use a soft tooth brush. Then just scrub the top of the apogee. If your using the storm. oh dear lord.... you need to take that apart and clean its injection heads. Most likely your going to have some funky gelly looking thing stuck. Also on your apogee.
Follow my cleaning and flushing guide. Use Vodka if your over 21. If not, get a bottle of Scope, and make your radiator minty clean
Another good method i learned was to use very hot water. Not boiling, but above warm, and flush it out of your radiator. This might be difficult if you lost your funnel. And it can get dangerous if you spill it on you. I prefer the alcohol.
And yes the alcohol or hot water will melt those gelly thing and flush it out of your system.
Have fun.... be paitent draining. It expect to take about 2 hours to drain properly. And remember if you used distilled with hydrX its non conductive if you spill. But please turn your system off b4 you do all this.