I didn't know, is the 340 in a 72 Challenger Ralley supposed to be blue?
340's went to blue in March/April of 71. So yes, 72 and 73 340's are blue. 74 360's are also blue.
There seems to have been a batch of orange engines that was misplaced at the factory. A few A-bodies have been found with original orange engines that were built after April 71. The assembly dates of the engines are a few months earlier then the SPD's of the cars they were installed in. It is thought that the engines were misplaced...found and installed in cars even though the change to blue had already taken place. I believe there was an intake manifold change that also corresponds to the color change time frame. The orange engine cars had the earlier intakes. I havn't heard of any E-bodys built after April 71 that had orange engines.
I didn't see any rust holes on the underside pictures. The trans is most likely the original one for the car. The missing piece probably doesn't compromise the integrity of the case. I personally wouldn't run it like that but it looks like it can be easily fixed with a piece from a donor case. If that trans case is original to the car, there's no way I'd replace it. I'd get it welded up.
Are you going to be bringing the car to the Cedar Falls show in a few weeks?