Your Cube facility will probably not work right under V1.41
See 
Nature Shrine Bug / Intelligence Bug
Predictive Targeting Center Temporal 
 Damage Modifier - System
"Targetting" should increase accuracy, not damage.  If you already had ~200% accuracy to hit a ship, then maybe you could get more damage by targetting structural weak points.
 
Time-Efficiency Center Temporal 
 Reduced Maintenance Cost - System
How about a "Temporal Decelerator" or "Cronoton Disruptor" for the same effect.  "Reduces the flow of time in the system, leading to reduced maintenance costs.  The device is turned off during combat situations."
Faith Shield
 Religious 
 Planet - Shield Generation
I reccommend that you replace "Planet - Shield Generation" with "Phased Shield Generation"
You get the same effect, but it is proof against PPBs.
Platforms
 Platforms
 Combat To Hit Defense Minus
No effect here; the planet already has a -200% defense modifier.
Bio Scanner
 Organic Technology
 Sensor Level (EM Passive)
Bio Cloaking Device
 Organic Technology
 Cloak Level (EM Passive)
How about "Chameleon hull" for the cloak?  I'm not sure what to call the scanner ("bug eyes")
As for all of the cloaks:
If those are racial techs, as I assume they still are, you would only be able to hide from alien races if you have every racial tech they have.
EG.  If you had a gravitic cloak, then Temporal sensors would see you.
If they are not racial techs, it would be possible to hide from anyone until you hit max tech.  Still, you'd have to research 5 different areas (and spend 200KT on your ship) to get an all-around cloak, while the defender needs only to research one area and place one component.