The route I was planing would resume from the original route after getting the first missle pack (MP). Then go down into Norfair, get the 5 MPs and the icebeam. Then go back to the first MP spot and resume on original route to get bombs. Or, if going for 40 missles, after getting the 5 MPs and the icebeam go left past the lift and get another MP, then on the way to the bombs either go up to the top of the gold column then go right and get another MP along the way, or go the normal way into the bombs, and then go to the top row and get the MP going left.
I don't know how all these secret passages work, but I think you may need to have bombs in order to get some of the missle packs in that 5 cluster and the icebeam there as well. If not I'm suprised you didn't do this route. If so I think you can still get 3 of the those MPs in the one row and maybe the icebeam, or maybe the icebeam requires bombs and the 3 MP row requires icebeam and/or bombs. If you could get those 3 MPs you could get the other 2 MPs described above to get 30 total missles.
Also, maybe the mother brain remembers it's damage when you leave and go back, then could do it with only 10 missles. Or, if the rinkas could give you missles the mother brain wouldn't have to remember it's damage.
I just found out that there's a bunch of special glitch rooms in this game that you can enter using this halfway stuck in door go through wall technique, I'm guessing none of this is usefull for a time attack? Here's a link for info about this:
http://www.cheat-database.info/display/walkthrough.phtml?id=1724