We're not going to be able to solve this for you directly. Your best bet is to try to draw a picture with as much information as you can ascertain. If there's a 3-way switch, there must be another one somewhere else, look at that. Find all the fixtures connected and look at what they are wired to. Turn off the power and see if you can identify which cables go where. Lamps and the fan will usually have fairly low resistance. You can unscrew the bulb(s) on the fixture you THINK you've identified and see if the circuit goes open. You can also find a wire tracer online or at better home centers that may help. Turn on the power and measure the voltages on the various wires. Once you have that you should be able intuit the correct wiring of the switches.

As an after thought, if you think the flow from the faucet is too slow, there is a fix. If you remove the spray head, there is a restrictor that can be removed or modified. It has three tiny, tiny holes that reduce the water flow. I enlarged two of them a bit with a twist drill so water comes out faster. (I hate waiting for the sink or pot to fill when I could be wasting my time on other things.) Two cautions: If you remove the spray head either have a helper hold on to the hose or what I did was gently jam a wooden spatula handle in the spout to keep the hose from dropping down the spout into the cabinet. Also cover the drain so the restrictor doesn't fall down into it. The restrictor is a small plastic insert about the size of a dime.

His response... “I know I made your day yesterday but... you just made mine! Very thoughtful of you guys but definitely not necessary. I really do love helping people and your kind words make it all worth it. BTW, Morton’s happens to be one of my Favs! I also feel as lucky to have you guys have the trust and faith in me to build your dreams! Thank you again!” ...and then we had a 2.5 hour conversation about my kitchen and bathroom cabinets. I’m sure things will come up during the finishing stage we’ve entered, and I’m ready and willing to forgive him for mistakes that happen. At least I know the foundation and guts of this house are 100%. He’s slightly OCD so things are pretty meticulous on the job itself. As he said in the beginning, he’s likes things more perfect than most homeowners he works with, so not too worried!

Wood thresholds are not acceptable on my builds. I have a good tile sub though, who I’ve worked with for many years. She runs one of the cleanest and most efficient sites around. Maybe your builder does not have a good tile person. Or he doesn’t know much about tiling. Unfortunately, you as a consumer are going to have to educate yourself, as this will turn into a contract dispute to get this redone the right way. Start at the Ceramic Tile Foundation, and read everything. Good luck!