If I wanted to update my layout so that the outer and inner loops would be connected, would I just add switches to connect them with a isolated piece in between the switches? Would I be able to run a train from the inner to the outer with each loop being controlled by one handle of my mth 4000, or will that be an isssue.
One channel (handle) of the Z4000 has enough power to operate two engines or the whole layout in TMCC and LionChief. Try putting the the TMCC signal lead on the Black output of the Z4000 where the track common is connected.
Bring the track drops to a common junction and connect them to the hot and common of the Z4000. Use something like the 50-1014.
No need to isolate the loops electrically if you want to join them. You should have the transformer set at 16-18 volts. Don't go a higher voltage with the Z4000. That can damage the Lionel engines.
Isolating the loops is only needed for conventional running (handle) or large engines that need lots of power.
The layout turned out looking nice! I like that you hid the wall receptacle with the mountain.