I will take a shot at your questions:
1. You will need a One Pass account for the miles to post, but you can switch them to your Mileage Plus easy enough, and then after the complete merge, not an issue. Status will not affect the card associated incentives.
2. It can't hurt to see if Chase will care about keeping your business on the Mileage Plus card by offering something, but worth a try. They will do a credit check regardless is my guess, though if you are concerned about being denied the Continental Card because you think that they will not offer additionsal credit limit, you can tell them that you will accept a decrease on the Mileage Plus Card or cancel it. I have done this in the past.
3. All speculation as you say. I am hoping no changes, i.e I like the FLEX EQM at no limit especially. Other posters have said there will be changes. If changes, hopefully previous holders will be grandfathered. I have the Mileage Plus VISA with the EQM which I am hoping to keep as well, but will give it up if the Charge Card EQM are limited from the two cards, then it won't be worth the fee.
Scott