I am creating missions where the player is mainly fighting dominion ships and obviously a miranda class just wont cut it... and I want to play the missions through realistically, not just click 'kill target'. Is there any way i can change my ship while testing foundry missions?
It is possible to level your Foundry test character. When you hit test map on say a space map, you can warp out and play regular missions for XP and once you hit 10 or 11 you can do doff missions.
You can also claim any c-store ships you may have bought. My test character is flying an NX class.
Realistically though I do not recommend testing combat balance in map testing mode because of things like BOFF and NPC pathing (which is not calculated until publish) and a bug where sometimes enemy npcs teleport to 0,0,0 coordinates. Best bet right now is to publish a test version and run it on your regular game characters to test combat.
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And if you do test with a test publish, I recommend against using your minmaxed PVE ship for testing combat balance because it will skew the results towards "too easy".
For my tests and reviews, I dug my T4 Galaxy-class USS Bajor out of mothballs and fitted it with a budget build. No weapons higher than Mk 10, no gear better than blue (apart from the freebie Obelisk warp core), phaser arrays, and quantum torpedoes.