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I'm working on an overwhelming project also, right now all my time is being divided between work and studying this project.
I saw you're using a MPU-3050 Gyro and I'm having the hardest time finding a good working arduino sketch for it.
Would you be kind to share your code for the MPU3050?
I think this is why ardupilot and matrix pilot (etc) use some sophisticated stuff to deal with all the noise, but that's only part of the issue. I've no experience with the MPU sensor. But there may be some things you can do to help reduce vibration noise if that's the cause. Balance your prop. Change how and where you mount the sensor package. Look at what quadcopter people do for sensor mounting. There's probably a lot of advice on ariplane sensor mounting / vibration damping, vibration isolation. Another thing is if you increase the resonant frequency you can low pass filter in hardware or software.
The lag you mention in software filtering... if you can increase the sampling rate it allows you to filter the same amount but with less lag. Well, there's much more to it I'm sure... I guess it depends on the frequency range of the noise among other things. If you know the freq range then you can start to forumlate a plan -- this is my guess, anyway. I've not actually had to do this because the on my ground rover, I found gyro sensors that were reasonably vibration resistant and so it was pretty much a non-issue.
Is the noise so bad that your algorithm doesn't work?