Your windows may hit the speaker if you mount them inside the door. They go quite low. There's many speaker options, including custom dash's.
X2 on adding a connector. I've seen a couple installs of power windows installed the same way.
'91 Frankenheep YJ. 4.0, 4" BDS, Richmond 8.8, Titan 12k, 35" KM2's, rust.
'88 YJ, 4.2/4.0 head, +4½" & shackles, BFG 33's (sold)