Ah, it would appear that the keyboard flex has been folded or damaged during the rebuilt process.
The caps lock light is controlled by one of the outer pins on the wide keyboard flex cable, as are some of the command and modifier keys.
Its quite common for the blue underlay of the keyboard socket (what is used to thicken the cable to help it seat well within the socket) to get bent or folded if not inserted perfectly in line with the socket.
Hopefully its not irreparably damaged the keyboard socket, as thats a big rebuild to undertake. But if you open the machine up again (make sure to disconnect the battery while working on it, then disconnect the keyboard cable. Clean the end with some isopropyl alcohol and look at the outer edge of the cable to look for bends or flexes, and straighten if necessary. Then very carefully reset the cable.
Make sure to lift and re-seat the locking latch at the back of the keyboard socket each time, and make sure that it is pushed in all the way. The visible traces on the cable should all be at the same point along the cable when looking closely at the keyboard socket. i.e. it should be deeper at one side.
That should solve the problem.
But in essence, the keyboard connects to the logic board via a USB controller bus, so it is a very simply device. The only point at which the communication is completely split out is at the actual keyboard. so when you lose specific keys like that, its either the contacts of the key (under each key is a rubber dome that inverts to make contact with a very delicate contact that can easily be damaged by liquid or physical damage), or the keyboard cable or socket.
I hope this helps.
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