Floor crafting failed

Currently, you are killing both items in the third command, and are then trying to execute on the killed items. This cannot work for obvious reasons. Assuming you are using the right items, i.e. setting the scores works as intended (check with /scoreboard objectives setdisplay sidebar craftss) you need to simply swap the third and fourth commands.

There are some minor other problems. If you have problems triggering the third command, you can try relaxing the radius constraint in the second execute in that command to r=1. Lastly, you are missing a space between the last ~ of the second execute of the fourth command and the following summon command.

There are a few problems with your commands. First, you can't have spaces in your datatag outside of strings, so you should remove the spaces in instances such as Name: "SpaceShipEngine" where they are not needed, and make the contents of your Lore tag a string by putting quotation marks around it. You also need to add a space between the ~ and / of ~ ~ ~/summon.

Not quite sure what you're trying to do, but you probably also want to swap the order of the last two commands; you're killing the items then trying to execute from them again.

The fixed commands should be:

/scoreboard players set @e[type=Item] craftss 3 {OnGround:1b,Item:{id:"minecraft:minecart",Count:1b}}
/scoreboard players set @e[type=Item] craftss 4 {OnGround:1b,Item:{id:"minecraft:dispenser",tag:{display:{Name:"SpaceShipEngine",Lore:["You will need this to start your spaceship!"]}}}}
/execute @e[score_craftss_min=3,score_craftss=3] ~ ~ ~ execute @e[r=0,score_craftss_min=4,score_craftss=4] ~ ~ ~ summon MinecartRideable ~ ~1 ~ {CustomName:"spaceship",CustomNameVisible:1}
/execute @e[score_craftss_min=3,score_craftss=3] ~ ~ ~ execute @e[r=0,score_craftss_min=4,score_craftss=4] ~ ~ ~ kill @e[type=Item,score_craftss_min=3,score_craftss=4,r=3]