1. Trader Rylee is glitch, so sometimes she will be transported to the debugging room. I had her coming to my town, but it's just up to luck. If you want to be sure, go with her until she gets back to the settlement.
2. You get your paint job after the Institute ending, it's an Institute exclusive feature.
3. Up to 5 Gauss rifles can be found at Skylanes Flight 1981 and Skylanes Flight 1665. You need master lockpick to get them from a hidden compartment of the far most trunk under the cockpit. Note that this cache contains leveled loot (causing different versions of the corresponding manifest to spawn). Players below level 30 are unlikely to encounter Gauss rifles at this location.
A Gauss rifle is found on the Brotherhood of Steel's ship The Prydwen. It may be stolen as soon as the player character gets into the ship from the ship's armory.
Carried very often by level 35+ railroad heavies whether in quests or defending the checkpoint objectives after siding with the Institute or the BoS, and rarely by Brotherhood power armor troops during Institute faction missions.
The Gauss rifle can be purchased from Weapons vendors after reaching Level 25.
A large quantity of Gauss rifles can be found during The Battle of Bunker Hill, as the constantly spawning Railroad and Brotherhood troops will carry them. One must however be quick in picking them up because NPCs will pick them up at the first chance.