Got this fixed. I skipped mapping the left/right trigger buttons (for some reason, the right one always ends up setting the left joystick button to the same thing as well). Once I did this, the controls started working properly.
Lagging problem fixed. I did as above but no change. I looked around in the retrorarch menu of the game. (Hot Key+X)
Settings-Video options. There was a setting for Vertical Refresh, and default was 60hz. It said that would be ignored unless video Threading was on. I turned on Threading and it fixed the lagging issue with no other ill effects thus far.
MITU you were a very big help on this and I really appreciate the time you spent to help me. Thank You
@yfzdude thank you for replying, I feel that I do have to research/find other methods of transferring ROMs to my Pi/RetroPie though than this flashdrive, because frankly I've had more flashdrives fail than MicroSDs! (blame the amount of moving parts I guess...).
@dv8mad You need to enable SSH first before using WinSCP - see the docs https://retropie.org.uk/docs/SSH/. After you enable it, then you can use WinSCP and transfer the CD images.
But you'll get the same result if you transfer the files over file shares, copying them via file shares in \\retropie\roms\segacd. Make sure that the files have the proper case, i.e. .cue vs .CUE, and the .cue file (which is a normal text file) also has inside the correct .bin filename. Remember that Linux has a case sesitive filesystem.
Once you have copied the files, restart Emulationstation and see if the system shows up with the games. If they don't, check the log in /home/pi/.emulationstation/es_log.txt via WinSCP and see if you get any errors there.
More information about Sega CD games you find in the docs - https://retropie.org.uk/docs/Sega-CD/.
@douga There's a very famous solution that's been around for a long time called Keyrah, you can check it out here http://www.vesalia.de/e_keyrahv2.htm . I know the C64 runs quite well on VICE but because it's such a famous machine there are better solutions around in FPGA if your life depends on a good modern version of the C64 in your original case. No real need to software emulate this one.
@BuZz yea i dont know any thing about linux except people that are smart with computers prefer it . Im trying to get in contact with then i cant get a response from loveRPI.I bought the whole starter kit with the control s heat sink and everything