I currently own a 2004 Mazda Rx-8 (Automatic) and have had it for about 9 months now and I had noticed that 1st and 2nd gear rev up fine but once i got into 3rd gear it takes forever to rev up when driving, 4th gear is fine too.

I had thought maybe a apex seal had blown but was told the car won't even start if it was blown.

I took it to my mechanic (not rotary mechanic) and he started messing with the computer and then the car wont turn on after that. I already purchased a new computer because I was told the computer might be bad because it shot out 10 codes when doing a diagnostic.

All in all, the car had no power in 3rd gear but still ran okay, just need feedback on why it had no power in 3rd but still ran fine? Carbon build up?

 

It's going to be important to know what those codes were. You very probably don't need a new computer and it's possible your mechanic is wasting your time and money.
Clues are in the codes.

Is the problem strictly limited to 3rd gear or is it rpm dependent? Does it hesitate at all at any point up to redline in 1st or 2nd?

Did the rpms increase in 3rd without an increase in acceleration? Or did the rpms not climb at all?

In automatic trans, gears are selected via solenoids. If one has gone out that would prevent you from entering or exiting 3rd gear, but it's possible something deeper in the trans related to 3rd specifically is not working correctly. If other gears work fine it's not the computer.

You're saying it doesn't start, what happens when you try? He may have just flooded it.

 

I've gotten it up and running now, but it continues to give me the P0335 and P0420 code and I deflooded the engine!!

Before the engine flooded it was taken in to check out the P0335 code and now getting it back started and new ignition coils in, the P0335 is still there!! I've changed the sensor and the connector to it and still hasn't changed!

 

you need to fix the p0335 before driving around
that could also be why you have no power
just to calrify, you already changed the eccentric shaft postiion sensor with a new one?
everything is clean around the area?

 

Did you clear the code and it came back? Perhaps the sensor is fine but the wiring to it is damaged.

Is the P0420 coming back as well? Because that's your cat and you're doing damage to the engine if you drive with a clogged cat. Best to take it down, examine and replace as necessary.