Most of the game's missions are pretty straightforward so I'll only go in depth as to how to acquire certain hidden parts. First of all there is such a thing as "corporate points" These little things help you gain so-called "clout" with certain corporations. The more you work for one corp. the more new parts they'll award you. Therefore unless you have a certain amount of points you may still not get the part until you come back later to finish more missions by the corporation that made the part. Blight's site covers all hidden part details here but I'll go into deeper detail on the ones that seem to have been giving people the most trouble.
Mission: Destroy Gun Emplacements
Hidden Part: Karasawa - Laser rifle
The first requirement to get the part for this mission is that you finish the first segment at a fairly fast pace. Remember, you can accept a consort with no penalties so the tank with the MG-500 is a great choice for backup on this mission.
First off I'll get into the design that got me through the mission easiest.
RACHIS(basically any head with mapping and a target point locator can work here)
IKS
MAH-RE/GG or CASK arms
TRIDENT or SHUT tank legs
FCS: ND-8(for it's long range)
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ROZ
CR-14 or KD99
DD/20
35 shot long range laser cannon(forgot model number)
this slot doesn't really need anything, extra ammo, or radar can be used here.
MG/1000
energy shield(doesn't really matter which one)
This design has good armor to outlast, a long range weapon to take out targets quickly from a distance, and a large ammo amount.
In the beginning of the mission activate your map, it should show where all your targets are located. After you see where they are located, switch to your laser cannon and shoot each target, I don't quite remember but one hit may be enough. Move forward as you shoot the gun emplacements with the laser cannon and if you lose them then resort back to the map. It shouldn't realy take more than 40 seconds to do this part of the mission, now for the next part...
After you accept the next part of the mission, get ready for some craziness. You must survive for 5 minutes straight while a constant onslaught of enemies throw everything they have at you. Basically keep strafing along the ground, use your shield to soak up damage as often as possible, and spray all the enemies with the MG/1000. Your armor and ammo supply should be sufficient for lasting through the ordeal. Again if the part isn't rewarded to you after the mission and you did exacly what I said, then you'll have to earn a few more corporate points later in the game.