I'm not too certain how you came to the conclusion that the long range firepower of the atlas being better at stock configurations here. The base model of the atlas carries a single LRM-20 as its one and ONLY long range weapon. The man up there put up a pair of LRM-15s, how in the world is that worse than a single LRM-20 launcher? Unless its only got 1 ton of ammo the LRM-15s can rain much better support fire.
However, the build by the OP is odd considering you're sacrificing medium range engagement power for close range punch on a chassis that doesn't have as much armor as the atlas. You're relying on the fact that yes you travel at 64 kph, but you gotta take note the fact that the stalker looks just as fat, if not fatter than an atlas. Hitting a 64 kph brick is much easier than hitting a 64 kph hunchback i'd imagine
I believe the original mech posted had dual LRM10s. This was upgraded once the list of available equipment was posted.
As for the stalker in question... eh. I'd rather keep the large lasers then gain 10LRMs, and I'm not sold on the SSRMs.
My personal Stalker build follows. Its my 'on the cheap' idea. No engine changes, no armor or structure changes, just weapons. Obviously, I'd probably switch to Ferro armor and max out protection, and make numerous other changes... but its the starting point.
LRM15 (2 Count) (Torso)
LRM10 (2 Count) (Arms)
Medium Pulse Lasers (4 Count) (Arms)
Medium Pulse Lasers (2 Count) (Torso)
LRM Ammo (7 tons) (840 Rounds) (16.8 Shots)
Double Heat Sinks (11 Count)
The LRMs are heat stable, The mediums are pretty close to heat stable. And it keeps with the Stalker's image - A massive Assault mech, slowly stomping accross the battlefield, spewing missiles. And just when someone gets in close, and thinks he's safe...
Well, you know how the story ends.