Both of your problems sound joist related. By that I mean, solid lumber floor joists used today are notoriuosly uneven. Your 2x10's could be off by up to 3/8 of an inch or even more. This is why so many builders of custom homes have gone to TJI's (trusses) because the quality of the milling has gotten so bad, along with lesser skilled carpenters who are supposed to check for that.
Anyway, how to fix.
1) This is what I would do. We're on the same page here. It's ok to change the direction of the plywood on a "patch". Just make sure you support the new and old section well and use nails (or screws) AND glue. BTW, 12" OC for floor joists is unusual. They must be spanned a little longer than normal to go with being that close.
2) For a 1/4" valley, I'd use fiberglass roofing singles and stack them up and taper them out as needed. Your subfloor and joists sound very stiff and solid so there is no worry there. And at 1/4" deep patch, you will still get most of the staple (nailing down the flooring) into the subfloor. I usually use my hammer tacker to staple down my shingles. This is an approved repair for fixing lows over wood subfloors with a 3/4" solid being nailed over it. You could use plywood and sand it down flush but more work. I just did this on a home where the addition subfloor did not meet up flush with the old subfloor. The roofing shingles fixed it in a jiffy, was inexpensive, and have had zero problems. OR, if you want to shim from underneath AND you have plenty of room to work, locate the offending joist(s) and drive a flat bar between the subfloor and low joist and pry up. Then drive wood shims in along the top of the joist(s) and refasten the subfloor (once it has been made flat) with screws. Simple but you do need room to work underneath. Oftentimes, there will be insulation in the way.
My long winded responce. Good luck.
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