My first experience with build tool was also like that, but recently I fixed some heavily damaged ships on moon surface and it's doable if you know how to do it, so this is what I learned so far:
- only use build tool to fix ship frame (make sure you have access to resources), it will automatically weld repaired beams
- you can't fix part if it's obstructed by something else (build tool fails probably due to parts clipping)
- universal tool has option in top right corner of blueprint tab to auto fill (icon on the left) missing ships parts with anything in vicinity
- auto fill seems to work only with basic components, so you may need to disassemble parts that were thrown off the ship and are still bolted to one another
- parts will be auto bolted, but it uses bolts in your bolt tool, so make sure you have enough bolts in your bolt tool magazine
- universal tool blueprint tab lets you turn off some types of parts, so they won't get in the way (you probably don't need to repair plates), these option may change automatically as you swap tools
- if all lose parts are attached and you are still missing some critical parts, you can craft them and just drop them from your inventory
- after everything necessary is attached use durability tool (blueprint tab top right corner middle icon) to check for any red components and manually bolt them to fix durability errors
- cables and pipes don't seem to be fixable, so use your tools to make bypass just to make the ship work cables / pipes blueprints can be fixed with cable / pipe tool by holding left mouse button and aiming at blueprint, but if the broken part is unreachable or too long, then just make a bypass (thanks Garth Zader for the tip)
- depending on how your ship was configured, it may suddenly start flying at full speed and crash as you keep fixing/modifying it, so either know your ship or prepare a way to quickly disable it (example: fcuForward lever left at 100 that got cable severed, or run out of fuel/propellant will make your ship fly instantly when you fix those problems)
- fly your ship to origin station and use repair terminal to fix it properly
- make sure your gameplay option to use safe speed on ships with durability errors is enabled
- sometimes durability tool won't work and if you have durability errors then you are forced to fly at reduced speed
- sometimes blueprint won't appear, but you can still fix the ship manually using tools
- storing ship in station and spawning it seems to fix the problem with blueprint not appearing
- if you can't craft some critical components on the spot and know the location of your ship (isan coords or screenshots of multiple station transponders) then you can use insurance transfer and deliver needed parts from origin station using some small ship (you can disassemble it near your ship and use the parts for repairs)
- if you need to deliver parts for repairs, make sure you bring enough stuff, so that your ship after repairs will have enough propellant, fuel, cooling to fly back to station, otherwise you may need multiple delivery trips and that would waste a lot of time
- in moon gravity ship falls down, but blueprint doesn't follow ship movements in real-time, so you have to wait for ship to reach the surface until it completely stops in hover mode
- in moon gravity parts dropped from your inventory will also fall and you will not be able to manually place them where you want (it will still work with blueprint auto fill), but you can solve that by dropping part on your ship and quickly bolting it anywhere, then unbolting - this will make it so the part is no longer affected by gravity
