Don has an excellent point on adjusting the brakes.

Is there any chance your brake pedal is hitting bottom on the frame or engine before it develops full hydraulic pressure?

The pedal should be able to go all the way to the floor without touching anything along the way.
Keep in mind the engine may torque over (due to decelleration forces as well as accelleration forces) - a little or a lot depending on the engine mounts you have.)

Looking at your photo it looks like things probably clear, but sometimes builders forget to stroke the brake pedal after the engine is in to make sure it's not hitting anything.

(This from a guy who built a remote oil filter bracket for a stock 50 Plymouth coupe and forgot to allow for the column shifter to go up for 2nd and reverse without hitting the filter can. Was kind of a bummer cuz the first bracket was aluminum with countersunk lightening holes. Next bracket was higher and rather plain, but it worked well. The offending - but good looking bracket hangs on the wall of shame with all the other failed ideas....)