When you figure out the section that won't pop up on the rim, don't screw around with liquid tire lube for too long -- go with the axle grease on that troubled section before you try and try and try and wind up kinking up your bead steel permanently.
And yeah, trim your excess bead lip rubber, it helps.
In contrast to Dave's recommendation, I would start seating the beads manually
at the stem with the troubled section intentionally winding up being located away from the stem, simply because all the heavy tire iron action should be away from the stem to keep from catching it or damaging it.
With the inner tube being held centralized by the stem, there is a lot more tire iron scraping of the tube rubber that will take place. By doing it away from the stem the tire irons simply push the free floating tube out of the way over to the free space that is available inside the tire.
And yeah, I put a tiny bit of air in the tube to keep it from having saggy wrinkles that tire irons jest love to catch and pinch through. Not enough to show on a gage, but enough to very lightly feel when you push the stem in.
This way you stand a chance of being able to poke the stem out the hole and have it to stay there without getting all twisted around or damaged by tire iron action levering everything against the stem hole. I would only thread the outer nut a turn or three so the stem can move freely in and out over the length of the free threads during the wrassling match
which you will take part in.
If your stem is cocked after the wrassing match is over, deflate completely but do so slowly while tugging on the stem to encourage the tire to move over at that magic point where it is inflated just enough to clear the rim and not big enough to seize its OD on the tire. Be patent, there is a zone where the inner tube is mostly floating free.
It generally takes a inflate/deflate or two to get the sucker go ahead and move back over to where it belongs.