if you update your profile to show your location then somebody might be able to help you better. There are several clubs here in England that do model railroad electronics and you might even be able to get a kit from them. MERG.co.uk is a good club with many circuits and knockdown component/kit prices.
You don't really need a circuit diagram for the circuit you want to build as it will have one microcontroller, a transistor(see below), voltage regulator with some filter caps and maybe some pushbuttons with pullup resistors. If you search on the web you will find many circuits.
Just bear in mind that a PIC can drive a single LED on a output pin, but current is limited to 20ma typically. As you are at model scale your lighthouse will most likely only have one LED, so you can drive that directly off the PIC pin without a transistor.
One of the smaller PICs should be able to do the job e.g. 12F675 or 12F1840. Read the datasheet. The circuits are very simple, which is the attraction of using microcontrollers - the same circuit can be used for many different projects sometimes. The downside is that they need programming (writing programs in C or assembler) and flashing the program onto the chip(need an programmer like a PicKit3 with development IDE like MPLABX).
The added advantage is that you get timers 'for free' to time your on/off/fading periods.
I am sure somebody here can provide you with a circuit diagram to just flash the LED, or even fade it on and off, without using a microcontroller, but I would make the investment in doing it with a microcontroller as it opens a whole new world of possibilities.
I developed a whole CAB control system using PICs and smartphones/PDAs/PCs to control my grandson's layout. It has a graphical interface, so you just click/tap on icons to make them happen or you can program entire routes at the click of an Icon.