Why did my blinkers and radio stop working after getting the engine replaced?

I recently had the engine replaced on my jeep
liberty 2004. When I got it back, I noticed that the
blinkers were out of wack, stereo not working,
interior lights and car alarm not functioning. Before
I took it in to get it fixed all of these things were
working just fine but the AC was giving out when
the engine started getting bad. The problem was
the AC only blowing out of the defrost vents. Now
the engine has been replaced the AC went back to
normal but now the other stuff stopped working
like it should. I went back to the mechanic to tell
him but was told he couldn't really do much since
he doesn't have an electronic machine to test what
wires are causing this. He also checked fuses
which all were good. He told me he could try and
fix it but he would have to do everything from
scratch again (not sure what he meant) otherwise
was told to go see a mechanic that knows about
electronics. He mentioned that before he started
working on it he did have to power up the battery
again since it had died and maybe that made
everything go out of wack but I've replaced the
battery before and that never happened. I don't see
how replacing an engine would make everything
else stop working, he said it doesn't make sense.
The right blinker blinks really fast, and the left one
doesn't at all but only lights up. The lights on the
roof top ceiling does not turn on or stereo. And car
Alarm is disabled. I tried unplugging the battery to
see if it would reset but it didn't change anything.
What should I do? :(