did you do a 30 day extension already? If not, then do that in Krabi instead of a border bounce. I've never seen any long ques at the The immigration office in Krabi, it's 1900 thb and quickly done. If you have an extension already, flying from Krabi to Kuala Lumpur and return is the most convenient.
Even though we know that some people have been approved with 1 month activities, we also know that others have been rejected with 1 month activities... This varies among the embassies/consulates so it is advisable to research the requirements of the embassy where you plan to apply. It is best to read all information provided on the specific embassys webpage plus using the search function in this group to read application-reports from that city.
If you can find a solution where you plan to spend most of your time (Phangan?) that is the best, since that will allow ATM-withdrawls inside the province without any fee.
The 90-days report is a "Notification of staying in the Kingdom for more than 90 days". It is done by filling in immigration form TM47.
"An alien who has been granted permission to temporarily reside in the Kingdom, if staying in the Kingdom for more than 90 days, that alien has a duty to report his/her residence to an Immigration Bureau officer every 90 days.
This is in accordance with Section 37(5) of the Immigration Act B.E. 2522."