massaging the headers is rather normal in just about every install. heck i even had to massage my headers to clear the bolt heads so i could install and tighten down the bolts on my 66 mustang.
the longer you can make the dimple, the better. that way you dont lose airflow at that point, or you can at least minimize the loss. some guys will flatten a long portion of the tube, or more accurately they will oval the pipe. this has the advantage of maintaining the pipe flow area while still gaining the required clearance.
speaking of clearance, as long as you have at least 1/2" of clearance with the starter, you should have no issues since you dont use the starter all that much.
another option to gain clearance with the starter is to heat the pipe up and bend it while hot to gain the necessary clearance. to do this you might have to R&R the header a few times until you get the clearance you need.
as for the starter itself, what you might do is head on down to the local classic car junkyard, and grab a starter off an FE engine, and bolt it to your motor to see if it fits the way you want it to. your investment should be around $10, which you can recoup by rebuilding the old starter and selling it on craigslist.
if you get a mini starter for your motor, get one that you can "clock" or change the position of the solenoid to provide clearance for the header.
