[jannes_z-28]

On you first question: I presume you are asking if you can mount the engine in to the car if the headers are bolted to the engine while you are mounting it. The answer is no. You have to first place the engine and then from underneat raise the headers in to its place. This means that the car has to be raised pretty high.
In some cases you have to unbolt the drivers side engine mount so you can raise the engine to make room.


2:
There is no problem to cut the flange, just use a hacksaw or cutting disc. What can be problematic is that the tubes could be under stress from the welding and that could lead to that the flange moves slightly so that they don't line up. No great problem but it could be more difficult to bolt them in place.

Edit:
I saw from another post that you asked about bigblock headers.
If you have a '69 with Bigblock it is important that you have the BigBlock engine mounts, other wise the headers wouldn't fit at all. If your car originally was a smallblock car you have the wrong enginemounts.

Good Luck

Jan