1-If I retreat my ship right as it starts to have CR drain, I will have less manpower on the field, and my other ships CR will drain even faster, and will get overrun faster.
That's not how it works. Retreating any given ship has no impact on the CR or remaining peak performance time of any other ships, allied or enemy.
Also another thing is that I should be able to retreat without completely eliminating my enemy while having a large fleet myself.
Yes, you can do this. Just retreat all your ships at any point; you don't have to eliminate the enemy to retreat.
2-Even still my enemy should of had a reduction in CR even more then I did, but when my ships were failing they were at like 60%
Your first post makes it sound like you learned some modspecs, but maybe never actually installed them on your ship. In the refit screen, do your ships say they have the Solar Shielding mod? If not, then there's no reason why the enemy would have had lower CR than yours. If they were running Hardened Subsystems, and your fleet isn't, they should have more CR than you did. Especially if you had been in a corona for a while before the fight, which drains CR very quickly.
3-That is essentially what I said, minus the combat stresses to the ship. What would that be?
There are lots of non-morale, non-damage things that the crew needs to do on a ship, which they can't do during combat. CR is partly the morale (in that morale goes down with extended fighting) but mostly the time it takes to keep the ship running at tip-top shape. Maintaining a ship costs supplies AND time. It takes time for the crew to reload the missile bays, scrub the fighter manufactory, eat a meal, recalibrate the ballistic targeting solution processor, de-irradiate the sensor array, replace spent fuel cores, QC the beam emitter fusion crystals for signs of harmonic phase degradation, re-magnetize the shield generator, de-polarize the flux vents, reboot the flux capacitors to check for stress fractures, etc. etc. They can't do this during combat, and it takes a little while to get to all these tasks. CR represents whether the crew has had out-of-combat downtime to get to these tasks. If they haven't, because they are stuck in combat, or because they are in hazardous terrain like a star corona, malfunctions start to happen. There's not really a morale mechanic in Starsector at all,
much to the consternation of some of us.4-I did not know of that. I have some doubts about that, but I don't think you'd lie.
Megas comes to these forums mainly to lie to newbies; it's great fun for us all to watch.