Only starts after sitting for 3+ hours

I can go out to my car and it will crank over every time no issues but.... only if the car has set for more than +plus hours then it will actually start and run like a top, until you shut it off. I can get it to start usually in a half hour if I mess around unhooking the negative and reseting the car but not always it's hit and miss a lot with this car. I have already bypassed the vats system correctly and nothing changed. It seems to start when the engine is cooler but not always. Sometimes I can't start it back to back 5 or 6 times but sometimes it won't start till you just let it set untouched for a few hours. Letting it sit seems to be the only thing that works for sure everytime. The fuel pump primes every Time I turn the key and the security light comes on for a few seconds then shuts off. Also the security light flashes when you open the door not sure if that's normal. It runs at normal temp and doesn't miss a beat when it is running. Thank you very much for your time reading this any suggestions at all that doesn't include taking it to a dealership would be upmost appreciated.