1. In theory one could leave just before the end of the 90 days and reenter. However, upon reentry an immigration official can take a hard look at the cluttered rubber stamps and bar entry for abuse of the 90-day term (I have never heard of it happening in Panama but it does happen in the US).
2. From the short stay, I have a feeling you did not wait long enough to have your picture taken for your 3-month card and you were supposed to get a Multiple Entry Permit under the old law. Depending on when you return, you may have to pay a fine.