Things are starting to clear up at the top, at least according to the CHN Pairwise Probability Matrix.
Michigan has clinched a #1 seed, with a 99% chance of it being #1 or #2 overall.
Minnesota State has clinched a #1 seed, with a 97% chance of it being #1 or #2 overall. Michigan is about a 60/40 favorite over Minnesota State for the top overall seed.
Denver can amazingly finish anywhere from #1 overall (0.2% chance) to #9 overall (0.1% chance). They are about an 80% chance favorite to get a #1 seed.
Minnesota is a 75% chance favorite to get a #1 seed, with about an equal chance at #3 or #4 overall.
North Dakota and Western are about 20% chance favorites to get a #1 seed. I have to imagine those 20% scenarios involve them winning the NCHC Title, while Minnesota falls in the B1G Tournament. However, at this stage, it appears likely they will both be #2 seeds.
Quinnipiac also looks destined for a #2 seed, with an approximate 72% chance. They have a very small (0.4% chance) of sneaking into a #1 seed.
The fight for the final #2 seed is likely between SCSU (60% chance) and Notre Dame (62% chance). I would guess that if SCSU makes the NCHC Frozen Faceoff (which would mean 2 victories over Duluth), they will get a #2 seed. The Huskies actually have a decent chance (~4.5%) of getting a #1 seed. I would imagine that would require them sweeping their way through the NCHC Tournament, with Minnesota losing in the semis.
Michigan Tech and Minnesota Duluth are likely #3 seeds (91% and 65% chances respectively), with the Bulldogs having an outside shot at a #2 seed (6.7% chance), and an even lesser chance at a #1 seed (0.5% chance). Of course, there is about a 4% chance UMD fails to make the NCAA Tournament.
Massachusetts is also likely (54% chance) to land at a #3 seed.
I have a feeling that there will be 3-4 "bubble busters" that will eat up the #4 seeds, although Ohio State (77% chance), Northeastern (64%), and Massachusetts Lowell (58% chance) are currently more likely to make the NCAAs than not.
Given all that, here is where things likely will end up, assuming no upset auto-bids:
#1 Seeds: Michigan, Minnesota State, Denver, Minnesota
#2 Seeds: Western Michigan, North Dakota, Quinnipiac, Notre Dame
#3 Seeds: St. Cloud State, Michigan Tech, Minnesota Duluth, Massachusetts
#4 Seeds: Ohio State, Northeastern, Massachusetts Lowell, Atlantic Champion
I would imagine something like this:
Albany:
1. Michigan v. 4. Atlantic Champion
2. Notre Dame v. 3. St. Cloud State
Loveland:
1. Denver v. 4. Ohio State
2. North Dakota v. 3. Michigan Tech
Worcester:
1. Minnesota v. 4. Massachusetts Lowell
2. Western Michigan v. 3. Massachusetts
Allentown:
1. Minnesota State v. 4. Northeastern
2. Quinnipiac v. 3. Minnesota Duluth