Hi George,
Congrats on your new bike! I don't own one myself, but my buddy has one that gives me all the frustration of ownership without any of the rewards (it needs 30+ years worth of maintenance done, but he doesn't want any money spent on the bike, by anyone). :>(
Your oil pump may have destroyed itself due to lack of lubrication, which will complicate returning it to stock even if the other parts are available. I would make the effort to put the oil injection back if it were my bike, but that's just a personal preference.
My MR175's air filter box was filled with shredded paper, mattress stuffing, etc. too. It wasn't until I found the acorns at the bottom that I realized what I was looking at (a squirrel's nest).
The 17212-358-000 OEM foam air filter is discontinued, but I have a spare/used one I can send you N/C if you want it. This filter was used for about a year, and cleaned twice (it still is in perfect shape). It fits over the cage, with the bottom edge of the cage fitting inside a slot that runs around the inside of the lower plastic filter edging. Provided the foam gasket in the bottom of the airbox is intact (it may not be), this setup should provide a very good seal. If the MT airbox is like the MR's, there's a metal screen that will prevent anything large from being sucked into the motor.
Here's an extremely condensed version of my parts procurement procedure:
1) Get a part number from Parts Nation:
http://www.hondapartsnation.com/pages/O ... 1000001//12) Enter the part number into the the Bike Bandit search engine to see if it's still available:
http://www.bikebandit.com/oem-parts3) If it's not, try eBay or Google.
If you're really serious about getting parts, you'll be able to find most anything you need - but some may not be easy. There are many actual MT250 owners here that will surely be able to help more than I will.
Ray