+1 to both points. Specifically regarding the repair person, repairing a stripped thread is not an uncommon repair, and any reasonably competent tech should be able to do that for not too much money.Off the top of my head I would suspect you need to push in and play with a lower basic pitch. If the MP is too far out, the short tube notes will be relatively flatter than the longer tube notes.
On the other hand, if your repair person is unable to make a permanent repair to a part with stripped threads because "a replacement part is not available", they may also have fouled up the key heights on these pads. (That wouldn't explain having the similar issue on tenor, but playing with a habitually too tight embouchure could.)
Regarding the flat B's, this sounds like a combination breath support and embouchure issue to me. Quick check on intonation - play B2 (middle line B, LH index finger, no octave key). Then "slur" to the same note, but finger low B. That is, overblow low B so it sounds the same as B2. If the standard B2 is flat compared to the B1 overblown, then turf3's comment is right on the money. Put your mouthpiece where you can switch between overblown B1 and B2 with no pitch change, then learn to play in tune with the mouthpiece in that position.