Sorry I'm just getting to this Andy,

First thing, IMO change the seal regardless.
That being said,a little excess crankcase pressure will generally not hurt your seal IF it is only a little pressure for a little time. If this has been going on for 1 year, I can't see the seal being any good. Of course, if you're so inclined, you can roll the dice and and pull just the tranny later if you want to.
Now, what's going on with the blow-by. You said the comp was good but the cylinder head was so warped out due to overheating? And yet your crankcase is so pressurized that you are blowing out seals and breathers? That's pretty heavy.
If your comp numbers were good all across (which seems a little strange for a head that was that badly warped), I'm wondering if you have a broken ring landing. Did you do a leak down on the cylinders before you took off the head? A broken landing can give good comp numbers but will leak down quickly. It's just that you are talking about a fairly fresh rebuild yet an overly warped head and extreme crankcase pressure. Or maybe the rings were not gapped properly on the rebuild.

I'm not bustin' your balls or anything on this. I just hate to have you do all the work of reinstall only to have the same problem. Do your cylinders look OK or are there any outstanding scrapes in the walls? I'm sorry if this is more than you were asking, I just had concerns.

MB