[Ragnarok]

In regards the retrofit question check out the newbie FAQ: Found here!

Here is what it has to say about retrofitting:

5.5 Repairs and Retrofitting
5.5.0 See also Section 14.0.2 for information on when the cost of retrofitting is deducted.
5.5.1 A damaged ship will be repaired if it is in the same sector as a planet with a Space Yard facility, or a ship or base with a Repair Bay or Space Yard component.(capnq)
5.5.2 The order in which repairs are performed is set with (F11) Empire Status/Repair Priorities. Clearing the priorities list will leave only the component types that you have the technology to build; more entries become available when you research the corresponding techs.(capnq)
5.5.3 The game chooses a ship in a sector to repair based on which ship has the highest-priority component broken, and then this ship will be repaired as much as it can. Example: say your repair priority list starts Vehicle Control (top priority), Engines, and Weapons. Say you also have two ships damaged in one sector. The first ship has only its bridge, a shield, and a piece of armor broken. The second ship has everything damaged EXCEPT its bridge, crew quarters, and life support (and does not have an Aux Con). Since the first ship has the a top priority Vehicle Control component damaged (the bridge), while the second ship has no Vehicle Control components damages, the first ship will be repaired as much as possible. Each turn the game re-determines which ship will be repaired (so that a ship that is repaired one turn may not be repaired the next turn). (Quikngruvn)
5.5.4 If a ship is fully repaired, any excess repair ability in a sector will be carried over to other damaged ships in the sector. In this case, the game will pick the next-highest priority ship as above, then repair it as much as it can. This process repeats till either all ships are repaired or the repair facilities/components have repaired as much as they can in a turn.(Quikngruvn)
5.5.5 Multiple repair bays will work on a single ship or base. Three repair bays fit perfectly on a Space Station. If they are Repair Bays 3, that's 24 components repaired per turn right there (with very low maintenance), which can make for speedy retrofits. Multiple repair bays on dedicated repair ships can greatly increase the lifespan of fleets at the front lines.(Quikngruvn)
5.5.6 Ships and bases can be retrofitted to another design at a spaceyard (located at a planet, ship or base). The Retrofit option appears under Scrap/Analyze/Mothball (hotkey G). The new design must have the same hull size as the old one, and have a combined total cost in resources of no more than 150% of the old design. Designs more than 150% apart can be retrofitted by designing one or more intermediate Versions.(capnq)
5.5.6.1 Q: How exactly do I retrofit?
A: a) Create your new design and ensure that the total resources (minerals + organics + rads) is not greater than 150% of the total resources of the original ship. If you want to retrofit to a more expensive design, you need to make multiple steps, each with no more than 150% increase.
b) Move your ship to a sector with a spaceyard, either planet based or on a ship/base works fine.
c) Click on any one of the ships in that sector then click the green triangle (retrofit, scrap, analyze, etc) (Hotkey G) for a new window.
d) Select the ship you want to retrofit, then click the retrofit button.
e) A new window pops up with all available designs that you can retrofit to. select your desired upgrade ship.
f) Click OK.
g) Your ship is now retrofitted and any new components must be repaired by the spaceyard. Once repaired you are good to go. Note that if you retrofit engines and you don't have a Resupply Depot on the planet, you could end up with a ship with 0 supplies because retrofitted engines come with no supplies.
5.5.6.2 You can choose multiple ships to retrofit, but all ships has to be the same class (The name you've given the design), after you've choosen them you can choose ships from another class in the same sector in the same turn and order them to retrofit as well.
5.5.6.3 It doesn't matter what type (Attack ship, defense ship..) you retrofit from, you can change type freely.
5.5.6.4 You cannot add a space yard or colony module to a ship that doesn't already have one. This can be turned on/off in settings.txt.

5.5.7 Units cannot be retrofitted. (capnq)
5.5.8 A faster, but more expensive, method to build ships is to use a retroseries. First, build a basic Version of the ship, usually taking a single turn. Then retrofit through a series of designs which gradually add components to the ship. Remember, though, that there can only be a 50% difference in total cost. If you are building a stellar manipulation ship (which has a single very expensive component), you can use any combination of components to get the total cost close enough to the amount needed to add the stellar manip. component, at which point the other components can be removed. (Krsqk, Imperator Fyron)
5.5.9 Engines that are retrofit to a different engine type lose all supplies, unless they also have Supply Storage components. Ensure you retrofit engines over a resupply depot.(DirectorTsaarx, Quikngruvn)
5.5.10 If you retrofit (captured, insurrected, or gifted) ships with special racial technology components that your race does not possess, you will lose those components.(DirectorTsaarx)
5.5.11 A space yard ship with a repair bay is an excellent way to refit ships in forward positions.(DirectorTsaarx)
5.5.12 Ships can't be retrofit while in a fleet (it caused problems in 1.49, and is not even possible in Gold). (Quikngruvn)
5.5.13 Ships with a space yard can’t build while cloaked but can repair while cloaked. (icon changes from “space yard” to “repair” while cloaked. The cloaked ship does not appear in construction queue. (Suicide Junkie)
5.5.14 Cloaked ships can’t be retrofitted.
5.5.15 Emergency supply & propulsion pods need a space yard (not repair bay) to repair.
5.5.16 Retrofitting a ship does not affect its crew experience.
5.5.17 Retrofitting cost 120%, 30% for component removal. This is seen only on the retrofit screen. (settings.txt)
5.5.18 Repairs cost no resources.
5.5.19 Space yard III and Repair Bay III both repair 8 per turn; all planet Space yard facilities only repair 5 per turn. Moral: better to repair in space.
5.5.20 Space yard ships can repair & retrofit while moving, assuming the ship it is repairing/retrofitting can move. Space yard ships cannot build while moving. Attempting to move a space yard ship that is building something results in an error message and no movement, building continues. (Suicide Junkie)
5.5.21 You can get ripped off on upgrading ships. Check that you are not upgrading engines of the same type from I to II or III - no benefit except lower maintenance cost, but additional retrofit cost. Master computers, almost the same thing, slight decrease in size is the only benefit, usually not worth the cost. Check every component to see if there is enough of a benefit to make it worth the cost.
5.5.22 Retrofitting a damaged ship makes sense, it had to be repaired anyway; may as well have it repair upgraded components. Also if a ship will take several turns to retrofit/repair, mothballing it will allow you to save on the maintenance costs. Don’t forget that mothballing will reset crew experience to 0%. For clarification, you can retrofit a mothballed ship or base. Sometimes it is advantageous to mothball the ship/base first before retrofitting so that you don't pay maintenance while repairs are in progress.
5.5.23 You cannot repair technology that you don’t possess (i.e. beyond your current research, special, racial, etc.) from stolen/gifted ships.
5.5.24 You cannot retrofit a ship which is carrying cargo even if the cargo components are not being changed.
5.5.25 If you fleet a space yard ship, you can't select the ship for building, but it continues to build what it was building. You can access the ship from the construction queue (button with the wrench on it) to alter the queue. (Suicide Junkie)
5.5.26 You cannot retrofit a ship to include a Colony Module or a Space Yard if one was not present on the ship already. (settings.txt)(Quikngruvn)
5.5.27 See also section 14.0.2. All refits, successful or not, are shown in the log as "vehicle retrofit". This can be misleading because the retrofit may have failed due to lack of resources or too much of a percent change in its components. You can only tell by highlighting entry and looking at center panel to see if it was successful.