Thanks for all the replies. Good advice for the banjo bolt pressure line.
Here is the problem I have with removing the 3/2 valves from the vacuum system. Namely, these valves are connected in two places to the transmission vacuum control valve on the IP. Do these connections affect only the EGR system, or do they affect both EGR and transmission? That is the question I have. Admittedly, I don't know how any of these valves are designed to function. It is obvious that they take vacuum and destribute it to various other components depending on how the engine is running at that moment. And I know that the whole point of the transmission vacuum system is to simulate the vacuum dynamic that is produced by a gasoline engine. Beyond that, though, I don't know anything more.
However, on parts sites like
autopartsworld the descriptioin for the 3/2 valve says it "CONTROLS EGR, INJECTION PUMP AND AUTOMATIC TRANSMISSION VIA VACUUM ROUTING COMBINATIONS."
So I am leery of just throwing away a part of the car which (as described) affects the operation of the transmission.
It seems clear that the transmission will shift no matter how much vacuum it is given. Mine shifted with none. But now that I went and put things back to where they should be it shifts a whole lot better. At least it feels that way.
The black box and EGR valve ARE ugly though.