Soft brakes when engine is running

As the title says, I am dealing with soft brakes while the engine is running on my 2000 Toyota 4runner. Prior to this my master cylinder went out. So I have replaced the master cylinder, brake booster, rear wheel cylinders. I have bleed everything properly, I have no air in my lines nor leaks, i do have vacuum on the booster. I have also bleed them several times for countless hours. I also took off the master cylinder and rebleed it thinking there was trapped air, and still nothing. Any ideas out there?

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@jordandom assuming all the bleeding etc. was done according to your Toyotas specs, I would check the brake lines specifically the hoses in the front. I have chased this myself for a long time, while the issue was a bad break line/hose to the front wheels.

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