Andy,
I just pulled mine two days ago. I used a paint heat gun and heat the block area around the base of the tubes. I'm not sure if it helped but I finally lost what little patience I have and then got a 6" pipe wrench and gently started tuning, first one way then the other. Finally they both came out........I would was lucky because I could feel the tube starting to give in on the sides.
As for the pickup, I have been told that there is a new oil pump that doesn't require a pickup tube going into the sump. Frankly I can't imagine how that works, but I got the info from a good source.
You can fix your tube by heating it with a torch, about an inch on both sides beyond the pinched area and gently hammering down a rod inside. This will round it out nicely. Make sure you pull out the rod
As for the filter pickup, I need to think about that one.
If you can post a picture it may be helpful to get our creative juices flowing.
Mike