The following is culled from my inventory files (which are more detailed to appearances, etc in individual issues) of Alpha's chronology.
Note, this is Alpha history as I have inserted it at times of publication, not a chronological list of publications!
I.E., (nit pick here?) the 1998 X-Men Alpha series doesn't chronologically fit continuity between both Alpha Flight and the X-Men due to memberships of the respective teams, so it is put in that area between Alpha Flight #1 and 2.
Alpha Flight #1 was written by Byrne to bridge the appearances between the disbandment of Alpha in X-Men #139 and a still-together team as seen in Marvel 2-in-1.
Many cameos, such as Northstar and Aurora being stricken by worldwide mutant attack, are not included, particularly when they had no speaking role. They were also seen in cameos several issues of Secret Wars II.


Alpha Flight #1-4–Sasquatch’s new team, Nemesis
Weapon X #22–Aurora, Box
Weapon X #18–Northstar
Uncanny X-Men #433–Sasquatch, Guardian, Vindicator
Weapon X #12
Weapon X #11
Weapon X #10–Director attacks Aurora
Weapon X #7-9
Uncanny X-Men #421422–rules of engagement
Weapon X #6–Director & Aurora
Weapon X #5–Box armor mass produced as concentration camp guards
X-Men Unlimited #45–birth of Heather’s Baby
Northstar joins X-Men in UNCANNY #414
Weapon X #1-4--Aurora, Wild Child
Wolverine #180–Shaman cameo
Wolverine #179–Shaman calls for Wolverine, a Puck shot
Citizen V: Everlasting #3–cameo
BLACK PANTHER #42-4--Heather established as pregnant in #43
Weapon X: Wild Child #1–Aurora institutionalized, partially recovered
Wolverine #173--Heather pregnant, Aurora kidnapped for Weapon X
Wolverine #172--Alpha Flight
Wolverine #171--Wendigo
Wolverine #170--Stay Alive part 1 of 3
AVENGERS #47--Marrina in captivity of Master
X-MEN #111-113–Northstar
Wolverine #143–Snowbird returns
Wolverine #142–Modok
Alpha Flight #18-20–last issue
Alpha Flight/Inhumans #1–Heather exposed to Terrigin mists
Sunfire & Big Hero 6 #1-3
Alpha Flight #9-17–Brass Bishop
X-Men #355
Alpha Flight #3-8
Maverick #3–Puck & Heather
Alpha Flight #1-2–Master
Domino #1, 3–Puck (does not appear in #2)
Wolverine #110–Shaman
Deadpool #1–Sasquatch
Generation X #19–Sasquatch
X-factor #116
Wolverine #92-95
Wolverine #83-84
What If? #62
What If? #59
Northstar #1-4
Alpha Flight #128-130
Death Metal #2--Alpha Flight
Death Metal/Genetix #2--Box
Alpha Flight #110-127
SHIELD #32–Wild Child
Alpha Flight #97-109
Alpha Flight Special #1-4--dual printing #97-100
Marvel Comics Presents #99--Puck
Alpha Flight #96
Marvel Comics Presents #92--Northstar
Alpha Flight #91-95
Avengers #321-324
Alpha Flight #62-90
Marvel Comics Presents #51-53–Heather, Wild Child
Alpha Flight #51-61
Alpha Flight Annual #2
Alpha Flight #41-50
Alpha Flight Annual #1
Alpha Flight #40
Avengers #272
Alpha Flight #29-39
Incredible Hulk #313--death of Langkowski
Alpha Flight #25-28
Iron Man #195--Shaman
Alpha Flight #23-24–death of Sasquatch
X-Men/Alpha Flight #1-2
Alpha Flight #20-22
Power Pack #9-10--Marrina
Alpha Flight #14-19
Crystar #11--Puck, Shaman, Northstar
Marvel Team-up Annual #7
Alpha Flight #9-13
Rom #56-57
Alpha Flight #2-8
X-Men/Alpha Flight #1-2--1998 series
Marvel 2-in-l Annual #7–Sasquatch
Incredible Hulk #272--Sasquatch
Marvel Two-in-One #84--Alpha Flight
Marvel Two-in-One #83--Sasquatch
Alpha Flight #1
Machine Man #18--Sasquatch, Aurora, Northstar
Uncanny X-Men #140--Guardian, Shaman, Snowbird
Uncanny X-Men #139--Guardian, Shaman, Snowbird
Hulk Annual #8--Sasquatch
X-Men #120-121
reprinted Classic X-Men #26-27--Alpha Flight vs X-Men
X-Men #109
reprinted Classic X-Men #27—lst Guardian
Alpha Flight Special #1--team's formation
Alpha Flight #-1--Puck, Wolverine, wedding of Mac & Heather

If you think different publications should be inserted differently for continuity, say WHY you think that, such as my above explanation for placement of the 1998 X-Men/Alpha limited. Reasonable enough?

My highest recommendations outside the Alpha Flight titles are:
1st X-Men/Alpha limited series/"The Gift" Trade Paperback
Marvel Team-up Annual #7
Avengers #321-324

Some of the most important outside appearances was Hulk #313 for the death of Langkowski, Machine Man for the off-panel beginning of the relationship between Sasquatch and Aurora, and the more recent Weapon X appearances.

Hope this helps some newer readers find enjoyable stories!