So, I know this is a bit of a backtrack, and for that I apologize.
This is my favorite Viper build- it does exactly what it is meant to. It's originally designed as a Deathwatch Kill-team support ship, but could serve equally well as a Rogue Trader vessel with minimal tweaking. It has two Archeotech components, which maybe makes it a non-ideal starting vessel- that and the total lack of armament. There is also a slight departure from RAW in this build, because the ship mounts two sets of Augur arrays- the second one cost an additional ship point to make up for it. This means that it has the W-240 passive arrays for stealthy operations, and when the ship wants to be noisy it can deactivate the W-240 array and energize the X-470 Ultimo array, which makes active auguries stupidly effective, particularly in conjunction with the Exploration Bridge. It has slave quarters, because originally chapter serfs, but the quality of components negates the morale penalty and I saw no reason to try to change it for the Rogue Trader.
A Miloslav drive, Warp Sextant and a Warpsbane Hull allow for fast, relatively safe warp transit.
A brig allows for captured targets, perhaps even a recovered carnifex or gnarloc. An Astropathic choir chamber allows the Astropath to do his thing. A Librarium Vault provides lore and research capabilities. Any of these could be swapped out for something else.
The crew quality is upgraded (because, again, originally Deathwatch), but you could save 5 points on that upgrade and install some extra components. You'd need to install more high-quality components to reduce power draw, unless you wanted to yank the Ultimo array, but hey- that's up to you. Depending on GM, you might be able to do something truly psychotic, like mount torpedo tubes (converting the dorsal slot to prow) with Guided torpedoes- with the Detection on this thing, you could probably do some nasty things with that.
All this in one, relatively inexpensive 49 ship-point package.
The stat block follows.
Speed 11 Man +30
Det +25/35 Hull 25
Armour 14 Turret 1
Space 29 SP 49
Mounts: Dor 1
Crew rating: Crack (40)
+5 to Active Auguries
+15 bonus to Silent Running manoeuvre
Any attempts to detect Viper suffer a -15 penalty at all times.
Additional -20 to detection attempts to detect Viper when silent running
No penalty to detection or detection-based actions when silent running OR +10 to detection, +15 to detect vessels with active augury, and +5 to enemy BS tests to hit this ship.
+10 to Focus Power for Astrotelepathy
+5 VU range to all psychic powers in space combat
Halve duration of warp travel, but events occur every 3 days instead of every 5.
When rolling for warp travel events, roll twice and let the Navigator choose.
+20 to all Perception tests to steer the vessel through the warp.
+30 to all Navigate (Warp) tests to steer the vessel through the warp.
+5 to any Intimidate tests as part of shipboard extended actions
+10 to any shipboard Investigation skill tests
Endeavour point boni
Criminal 50; Exploration +50; any objective where hauling prisoners could be useful +25
Build worksheet (I apologize for any column issues, I think I got it to behave, but I don't really trust it).
Component Power -- Space 29 SP 27
Cypra pattern drive (Archeo) +40 40 -12 17 +2 29 (BFK)
Good Miloslav Warp Drive -8 32 9 8 1 30 (BFK)
Warpsbane Hull 2 30 0 8 1 31 (core)
Repulsor Shield 6 24 1 7 0 31 (ItS)
Exploration Bridge 4 20 1 6 1 32 (ItS)
Slave Quarters 1 19 1 5 0 32 (HosAcq)
Good Vitae Life Sustainer 4 15 1 4 1 33 (Core)
W-240 Passive Detection Array 3 12 0 4 1 34 (HosAcq)
Good X-470 Ultimo Array 5(0) 12 0 4 2 36 (BFK)
Warp Sextant (Archeo) 4 8 1 3 2 38 (BFK)
Good Empyrean Mantle 2 6 0 3 3 41 (ItS)
Astropathic Choir Chamber 1 5 1 2 1 42 (core)
Librarium Vault 1 4 1 1 1 43 (core)
Brig 1 3 1 0 1 44 (BFK)
Crew to Crack - 3 - 0 5 49 (core)