dang why did you vandalize your PS2 with all of that red stuff written on it also, it would really help us readers out if you could start breaking your post into smaller paragraphs to suffice for a better reading.
i think that your having problems because your flip-top lid is somehow crooked or misaligned (because of the way that you made it or the top case has a different fit on the console since it's a different model). you could use the older (original) spindle that you've used before to give a better grip on cd discs.
anyway, i have a more of a commercial flip-top lid installed on one of my consoles. i had to swap out the cheaply made plastic spindle with the original one in my case. the spindle serves as a sort of security check (from what i've heard before) and it keeps the disc from flying out like a weaponized Japanese star.
the best solution would be to go on ebay to buy a commercial flip-top lid.
PS1/SCPH-7501 | MM3 modchip
PS2 v9 | 250GB hdd | PS3 component cable | katana 32mb mc
PS3/CECH-2001B | 250GB hdd | 3.65 ofw