Need help diagnosing my civic.

Info: tie rods, brakes and suspension were replaced before this issue. Also got an alignment done.
However, 10-15k miles after wards i was experiencing vibration when braking and engine randomly dying on me and turns out cam shaft broke in half so replace the head. Since then ive been having this issue.

I have a 2000 civic MT, it starts and drives fine in the morning when i go to work except when im going up hill, 5 gear struggles so i have to down shift every time.

Problem is when im coming back home during the afternoon. Car starts fine but after it passes 40mph, the car shake and vibrate even when braking to a stop. When i shift to 5 gear it feels like the car is loosing power and struggling to run so ends up driving on 4th all the way home

 

the word "brakes" is very general

what was replaced?

from the description, i would assume the rotors are bad

 

brakes and rotors both replaced