Visa for 90 days. Do I need to go to HK or I can stay in Shanghai? where to apply?

Marco, if you apply from the local entry and exit management bureau, I am afraid that you may just get 30 days L type. If you go to HK, I am not sure if you can apply there because the rule requires that the applicants there must provide their Hk resident status. Perhaps, you might find an agency in Hk to help you apply. But there is no guarantee that you will get a 60 to 90 days L type successfully. The cost will be much higher.