My power windows and dome light and door locks wont work and it wont shift are all those problems on one circuit breaker or fuseable link

You say the driver window works? wouldn't be a main fuse or fusible link then -driver door locks and window wouldn't work either. Each door has a module inside (computer) . The driver door has a circuit breaker power feed an a fuse DDM fuse 10amp located in rear junction block circuit breaker is located in under hood maxi fuse block. The circuit breaker also feeds battery voltage to the other door modules too. PDM - passenger door module fuse 10amp located in the instrument panel fuse box and the RDM - rear door module RDM fuse 10amp located in the rear fuse box - under the back seat.

Each power window is connected to a permanent magnet motor. The motor raises or lowers the glass when the door module applies voltage to the motor. The direction the motor turns depends on the polarity of the supply voltage provided by the associated door module. The 2 front doors have their own separate modules. The rear seat contains a single module, which controls both of the rear power windows.
A serial digital communications link, called the simple bus interface, is used for communications between door modules and the driver's door power window switches. The use of serial digital communications allows the use of a single wire to convey switching information between the power door lock switch and the driver's door module (DDM). The serial communication is also used in order to transmit switching information from the DDM to the other 2 door modules.
The door modules apply battery voltage of the correct polarity to the respective window motor when any local, or power door lock switch, UP switch is operated, driving the window up. Battery voltage is applied to the respective window motor in the opposite polarity when any local, or power window switch, DOWN switch is operated, driving the window down.

Driver Door Module (DDM)
The driver's door module (DDM) directly controls the driver's door window motor and the express down window feature. The DDM sends window UP/DOWN messages received from the power door lock switch to the passenger door module (PDM) and to the rear door module (RDM) over the simple bus interface (SBI) line. The DDM also contains a class 2 data link which communicates with the other vehicle system modules. The left front power door locks and the outside power mirror are also controlled through the DDM.
Passenger Door Module (PDM)
The passenger door module (PDM) controls the passenger's door window motor. The PDM controls the passenger's door window directly from the right front power window switch or from instructions over the simple bus interface (SBI). The right front power door locks and the outside power mirror are also controlled through this module.
Rear Door Module (RDM)
The rear door module (RDM) controls both of the rear door window motors. The RDM controls the rear windows directly from the rear door window switches or from instructions over the simple bus interface (SBI).

Beings as everything that stopped working is on the passenger side, I'd think some wiring got disconnected or broken.

Check you fusible links and circuit breakers. Not sure how you put the alternator on but you must disconnect the battery while hooking up the alternator.If you connected it wrong or arced it against something then its possible you popped a fusible link. Use a test light and test on both sides of your fusible links. Try that and see if it helps.

under the drivers seat is the seat control module

Check condition of fuseable links at battery possitive. check both ends with test light as they may look ok but be open circut inside

Check your fuse box and the underhood circuit breakers and fuses. Some are interchangable
so be carefull and if you have an ohmmeteter or a continuity tester check for voltage or
no voltage. Most are well marked with what they protect and what amperage the replacement
should be. You may also have a bad fuseable link. Check with your autoparts store and have
them lookup your car's "Fuseable Links". Check them if all else fails.
Good luck

I don't really see a dedicated fuse or circuit breaker for the moonroof. I do see a 30 amp circuit breaker for the mmonroof but that also controls the power windows and the sliding back light as well as the moonroof, so if you're not having problems with the other stuff I would say it's not the circuit breaker. There is a 10 amp fuse for the delayed accessory power for audio, power door lock switch & the moonroof switch illumination. The 30 amp circuit breaker is located in the number 401 position in the passenger compartment fuse box (see picture below) and the 10 amp fuse I was telling you about is in the number 22 position. If it's just the moonroof itself I would check to make sure the switch itself is good or even the motor could be bad. I see no fuseable link going to the switch but that's not saying there may be a bad wire so check for power to the switch. Wish i could have been a little more help but in this case this is all I can give you. I hope this helps and good luck. Here is your picture:

There could be a timed circuit breaker:

Circuit Breakers The headlights are protected by a circuit breaker in the headlamp switch. If the circuit breaker trips, the headlights will either flash on and off, or stay off altogether. The circuit breaker rests automatically after the overload is removed. The windshield wipers are also protected by a circuit breaker. If the motor overheats, the circuit breaker will trip, remaining off until the motor cools or the overload is removed. One common cause of overheating is operation of the wipers in heavy snow. The circuit breakers for the power door locks and power windows are located in the fuse box.

It sounds like you may a faulty door lock switch. If you pushed the switch to lock the doors and the switch stuck and kept door lock solenoids energized, that would drain the battery. It would also keep the door locks from unlocking, as to why window don't work it could all be on the same fuse or circuit breaker. Usually the power windows are on an automatic reset circuit breaker. Do you hear click and a short time later another click (with the battery charged)? If so that the circuit breaker tripping then resetting. Good luck!

first of all power windows usually are on a circuit breaker... did you check all fuses under the hood in the power dist center.. power door locks are not on the same circuit as the windows first i would pull up the window switch to see if you have power on it.. let me know