Is that a new cam chain or the used original? If it's used, it's probably stretched and that's why you can't get the cam notch lined up perfectly. Your valve and ignition timing won't be exactly at spec. Whether it's off enough to effect the way it runs, I can't say. There's lots of these running around with stretched chains and they seem to keep on going.
Can I ask why you're replacing the points and advance housing seals? Were they leaking or do you just have them and figure WTF? The new seals are supposedly improved, with a triple sealing lip, but reports on them aren't all good. You'll notice the seal is pressed into the housing as deep as possible without hanging out the back. The ends of the cam that the seals ride on don't stick out much so the seals have to be set in deep like that. The problem with the new "improved" seal is that they added those extra seal lips on the outside. Sometimes they don't even make it onto the cam stub so are no help. The new seals can be leakers.
If the old seals weren't leaking, I wouldn't replace them. It is something you can do any time in the future with the motor in the frame if need be. If they had minor leaks, cleaning the end of the cam where the seal lip rides by buffing it with a Scotchbrite pad will often cure the leak.
But, if you must replace them, it is pretty easy, one of the easiest seal replacements on the bike I think. Cut two small squares of plywood, one big enough to fit over the front of the housing, one big enough to fit over the seal and it's bore on the back. Find a suitably sized socket that just fits the seal. For removal, "stack" the larger piece of plywood against the outside of the housing and the socket against the old seal on the back. Place this "stack" in a vice and slowly tighten it. The socket will press the old seal out and into the housing. For install, use the large plywood square again on the front and place the new seal and smaller plywood square on the back. Into the vice again and slowly tighten. The little plywood square will press the new seal into the back of the housing. Leave it out a hair more than flush, so you can see the rounded edge on the seal. Remember, that new triple lip needs all the help it can get to make it onto the cam stub.