There is a sort of pilot within the pump that the tube fits into. You may have been hitting the taper just before that pilot, making it seem like things were not aligned. Loosening the nut which holds the pickup in the pan also helps.
If you have assembled something once with no problem and took it apart with no apparent problem, yet you find that you are having to force it back into position during reassembly, then there is probably some other issue preventing it from going together correctly. Never, ever force anything unless you are absolutely certain that it is what must be done.
Bending that tube is not a good idea unless it is done in a controlled manner. If you make a bend on the outside of the pan, you have to be absolutely certain that no movement occurs within the pan while making the bend. Otherwise, you change the relation of the pickup within the pan and that can have a detrimental effect on oil pressure by placing the pickup too close to the floor or pulling it out of the oil.
Depending on how it is now bent, it may not be concentric with the pump which may pull the seal slightly one way or another, preventing a good seal.
One thing you can try to see where your pickup is now located is to put modeling clay in the bottom of the pan, put everything together like normal then pull it back off and observe the imprint. You can then measure the imprint to determine the clearance to the pan floor. The problem with doing that with a Y block is that it is hard to fit the pan and pickup without moving the pickup, which would make a false imprint into the clay.
If you are good with math measuring and have the appropriate tools, you can measure the location of the oil pump inlet in relation to the pan rail and use that to setup the pickup in the pan just as it would be when installed on the engine, being sure to take into consideration the gasket thickness. Then you can see exactly where pickup is positioned. This will not work if you are not confident in your math skills or cannot get accurate measurements. The oil pan's rail must also be perfectly flat for this to work.
It may be easier to get another pickup, install it with a rubber seal and go from there.
Lawrenceville, GA