To get the shields to work, make sure you have something like this (extracted from my armored transport mod):
<snip>
shield_link = l_freighter_shield01, HpMount, HpEngine01
hp_type = hp_freighter_shield_special_10, HpEngine01
hp_type = hp_freighter_shield_special_9, HpEngine01
hp_type = hp_freighter_shield_special_8, HpEngine01
hp_type = hp_freighter_shield_special_7, HpEngine01
hp_type = hp_freighter_shield_special_6, HpEngine01
hp_type = hp_freighter_shield_special_5, HpEngine01
hp_type = hp_freighter_shield_special_4, HpEngine01
hp_type = hp_freighter_shield_special_3, HpEngine01
hp_type = hp_freighter_shield_special_2, HpEngine01
hp_type = hp_freighter_shield_special_1, HpEngine01
<snip>
If your thruster isn't working, check the power supply you are using for the ship.
[Power
nickname = vic_armored_power
ids_name = 263713
ids_info = 264713
volume = 0.000000
mass = 10
DA_archetype = equipment\models\hardware\li_fusion_reactor.3db
material_library = equipment\models\hardware.mat
capacity = 10400
charge_rate = 1240
thrust_capacity = 0
<- 1000 is default
thrust_charge_rate = 0
<- 100 is default
lootable = false
If you have thruster capacity and charge rate test it in the game, if you see the smoke trail from the thruster but it just isn't moving your ship check your engine...
[Engine
nickname = vic_armored_engine
ids_name = 263885
ids_info = 264885
volume = 0.000000
mass = 10
max_force = 240000
linear_drag = 3000
<- compare this to your thrusters force
<snip>
If the engine's linear_drag is too high the stock thrusters simply don't have enough power to move the ship, they were designed to work with a liner_drag of 599 not 3000
You could fix this my redoing the linear_drag or adding more thruster hardpoints, you'd need 5 to get the same result from your thrusters as a fighter does, but then it would burn through your capacity 5 times as fast so be prepared.
If the thrusters still won't work then your hardpoints are screwed up. I think the thrusters, mines and countermeasures all need to use fixed hardpoints and if you're just using running light hardpoints they may have a bad orientation but they should still work, not sure what will happen if you put them on a regular weapon or turret hardpoint.
I just gave the AT enough armor to make the Titan jealous and it's the only ship in the game than can mount a class 10 freighter shield so I figured not having thrusters, mines or countermeasures was a good balance, besides... with 9 turrets it's kind of fun trying to shoot the incoming missiles instead