Is it safe and okay to use the stock JBL speakers with an aftermarket cd player of 180-200 watts? Or do I need to get aftermarket speakers as well, and what about the stock amp, can I use it or will it blow my speakers etc?

Well if you want the stock speakers to work correctly you have to use the stock amp. The amp has all the crossovers internally. They say that hooking an aftermarket stereo to your stock amp will eventually burn the amp up, but it can be done. I just used a 4 channel amp to run all new speakers. Sounds good too.

can you install a new amp with stock wiring?

can you install a new amp with stock wiring?
Nope.

Well if you want the stock speakers to work correctly you have to use the stock amp. The amp has all the crossovers internally. They say that hooking an aftermarket stereo to your stock amp will eventually burn the amp up, but it can be done. I just used a 4 channel amp to run all new speakers. Sounds good too.

You can use an after market amp with your stock speakers, but you would want to add bass blockers so you don't blow the tweets.

i don't have jbl and replaced the deck (cheap ass pioneer for now) and front speakers (alpine type-s) and was told that my amp is wearing out because of the deck and wanted to replace it, but I wanted everything to be reversable.

i have a 250W head deck and the stock jbl tweaters and stock amp (for speakers) and its worked fine for me and i blast it everytme i am in the car and it sounds great still a summer and a half later, but i am forced to keep the volume at a certin hight because of an over powered sub i have...... so i never relly had to strain the speakers that hard..... but I think they should be fine for awhile if u leave ur stock amp, if you have the jlb's they are acculty very nice speakers just listen to um you will hear um befor they blow in most cases and just keep the volume under that.