Something seems wrong. You originally mentioned that when you check first you got a CRS score of 390 and now when you checked again with CLB 9 you only got a 3 point increase?
If you look at the CRS scores document it says for 3 years of foreign work experience you will get 25 points with CLB 7+ and 50 with CLB 9. I’m assuming you are married and have 3 years of foreign work experience so it’s a 25 point increase.
Also for an MS degree, you would normally get 25 points but with CLB 9 you will get 50 so right there you have a total of 50 more points bringing your score to 440?
Finally, there are many PNP progs one for each province each is very different some are focused on specific skills others more open.