I am replacing two kitchen lights. each light has a separate on/off switch on the wall. both have the same circuit breaker. I replaced the 1st light and all was well. There was light. I removed the 2nd light which was a 4 bulb florescent pillow style, this one has lots of ceiling box wires, 2 black, 2 white, 2 ground and 1 red. I capped 1 black, 1 white, 1 red and 1 ground and used the other three to attach to my new fixture. I had no light. I then started with the black wires and unhooked my two blacks and took the cap off the third black and used that black with my light fixture black and capped off the other black. Now I have light at the second light fixture but now the first fixture is not lighting.
I then try using my two black wires (one from the box and one from the fixture) and added the red wire. Fixture #2 still works but fixture # 1 still not working. At this point I can now turn fixture 2 on and off with both wall switches.
I have rechecked all my wiring and caps and all appears fine.
Both new fixtures are 3 wires, black, white, ground.
1. what wires should I be using at the 2nd light?
white, black, ground? What do I do with the extra wires, white, black, ground and red?
Why did the 1st black wire from the ceiling not work but the second black wire did work?
2. why is the #2 light working on both wall switches?
3. Why is fixture #1 not working since I remove the florescent fixture and installed the new fixture?
4. Are there wires that are at fixture 2 ceiling box that also control the light at fixture 1?
Thanks for the help.

What's going on is that power is fed into that box and split between the two switches. As to tell you what to do, not going to happen over the internet. If you have a meter and some electrical knowledge, then disconnect all you have done and identify all the wires. If you can't do that then call in an electrician.