97 4 cylinder Honda

Hello,i changed the motor on this little 4 cylinder Honda, I never disconnected any brake lines but I did have to pull a vacuum hose off the brake Booster and when I did the it drained it's pressure as in (air from the brake booster) When I removed the hose. The other end of the hose connects on to the throttle body. So after putting new engine in and hooking back up that hose the brakes seem to one quarter work.... the brake pedal ant soft or anything. I bleed the brakes on the front etc and it didn't change any thing. Any idea. It's a 97 4 cylinder Honda