To reverse a face you right click on the face and there should be an option "reverse face".
To merge 2 objects together, they need to start as solid objects. Using a plugin like solid inspector is a good start. If you have 2 solid objects, you can use the solid tools that are built in to sketchup.
The way that I found your your inner faces was to delete the flat planes one at a time to look for additional faces below it. To restore a flat plane, you only need to redraw one segment of its perimeter.
I really suggests getting the solid inspector plugin from the extensions warehouse.
Also look at CADspan
SD3 w/ mods:
Glass bed with QU-BD heat pad upgrade, threadless ballscrew w/ 8mm smooth rod, spectra line belt replacement, lawsy MK5 extruder, Lawsy replacement carriage, E3D hotend, Ramps 1.4 w/ reprap discount controller, DRV8825 drivers, 12v 30A PS, Acrylic case, Overkill Y-idlers, Filament alarm, Extruder fan + more.