You have it all basically correct
So I can prepare wisdom mod (lets say +3) + level per "instance" (before doing a long rest). (So I can prepare 6 spells)
Yes, you would have 6 spells prepared each day. However, you get your spell slots back and you get to re-prepare spells after a long rest, not before. You would need to complete the entire long rest before you prepared new spells and got your used spell slots back.
I can choose any 6 spells out of the level 1 and 2 list (since I only have level 1 and 2 spell slots)
Yes, there are no restrictions on which spells you can prepare, so you can prepare all level 1 spells, all level 2 spells (although that isn't a very good idea with only 2 level 2 slots), or any combination of the above.
I can cast the same spell as MANY times as I want (like I can cast goodberry (a lvl 1 spell) technically 6 times (4 level 1 spell slots, and 2 level 2 spell slots). The level 2 slots will increase the damage of course.
Mostly correct. Not every spell increases in potency when cast at a higher level. In fact, the Goodberry spell you mentioned does not get any better when cast using a level 2 spell slot. Many do, but some do not. Keep that in mind and make sure to read the spell description before you use it in a higher level. To be clear, you absolutely CAN cast a low level spell in a higher level slot, however if there is no additional benefit for casting the spell in a higher level slot (as per the spell description) then you may not be optimally using your limited spell slot resources.
but I could only cast spike growth (a level 2 spell) 2 times, because I cannot cast it as a level 1 spell.
I could do a long rest and re-prepare 6 more spells and my spell slots would all be refreshed.
Yes, with one minor caveat. Keep in mind that Rules-As-Written, it is not the player that decides to take a long rest, but the DM/GM that decides if a long rest is available. Make sure you know how your DM is running the game, because you cannot initiate a long rest without DM approval, and that may determine how you use your spells and which spells you prepare.