Jesus, no one here is interested on low power, N/A engines?

event to give some advice? well, I went ahead, and bought a 4E-FE first gen, to replace the old 2E that was on the corolla. I didn't like the way the delivery guys behave with the engine, I think they broke some little things, or worse if something went loose on the engine, and fell. Here are pics of the one I got:
questions:
in picture #2 there are 2 little holes surrounding the little pipe, with cut hose, I dont know if these two holes carried a pipe, is this normal or do I need the pipes?
on the last picture there's a little rubber part, I dont where it goes (havent try hard to fin the place anyway) and the question is that if it is something important enough to worry about.
I didnt got the transmission, because I wanted to use mine, but the one that was mated with this specific engine, seem to have some connection to the harness of the engine, will this represent trouble for the ECU to not work properly??
old 2E didnt use a ECU, as said before, is an early model, it even used a point breaker type ignition. Any help appreciated.