Welcome! Sorry to hear about your troubles here - they seem somewhat atypical. The alarm problems may be caused by a faulty alarm unit. The control unit is placed underneath the driver's seat, and as such, when it rains and the roof is open or leaking, water will collect in that area causing major problems.
A flashing check engine light is a serious condition that indicates a misfire (of course, you mentioned that you can hear this too). Don't drive the car in this condition, as there is the potential for raw fuel to be dumped into the exhaust, which can then ignite in the catalytic converters and cause major damage to them. The best suggestion I have is to get a code reader and see what the car is trying to tell you. See this article here:
Pelican Technical Article: Reading Boxster Fuel Injection Fault Codes / Diagnosing Problems - 986 / 987
Let us know what you find out!
-Wayne