My memory is a little hazy on those steps, but iirc I think I had some similar slight mis-measures like that too. I think they probably come about from doing the cutouts on the central joint.
Before anything make double sure the template didn't get stretched any (I had to scrap my first try because the wet glue was warping everything) and none of em are upside down or nothin, but yeah after that, I'd say some slight forced adjustments are normal. Remember they're only supports so it's ok if they're not perfect as long as the height is good.. It's the bases themselves that have to be perfect, since that'll be what everything else attaches too. Technically you could even build without the supports, though it'd be a pain and easy to accidentally cave the whole thing in while you're wrapping the outer layer.
I think actually when I did it I just sliced off all the inside sections of the supports, so there would be like an empty circle in the middle of them all, then aligned them by their outside edges to the base edge; since that's the important part for the wrap. Like this:
[ATTACH]68849[/ATTACH]
The only part you gotta be careful with are the transversal supports for the cheek area, since they're spossed to overextend on the bottom to keep the wrap completely round (see that post above a bit), maybe keep those the full length. Or as long as the edge is aligned to the top base I suppose it's ok either way too.
Another mis-measure you'll likely to run into too is when you wrap the outside panels around the bases, nearly everyone gets a few mm gap in the rear above the keyhole (if it's like an inch though, that's a problem). Also the cheeks and dome are likely to be very difficult. Pretty much everyone except antman and his magic cardboard has trouble there. Bondo fixes everything though. 
