High frequency output via port manipulation while reading from a sensor.

I'm a beginner at using Arduinos, but need to do this for a school project that involves them. my problem is that I need my board to preform three tasks, but one of them seems like it will involve port manipulation, and I'm unsure if it is possible to read while using port manipulation to output.

I need a high frequency signal to control the power supply, between 500kHz-1MHz. I could do this with a oscillating circuit, but that will further bulk up my design, which I'm trying to avoid. Then I need to read the output from my sensor, a Geiger-Muller tube, which maxes out at 10,000 counts per second. And finally I need to output the reading from the sensor. I'll be doing something simple like an LED or speaker, but in both cases a signal would need to be output only every 100 counts, to use the analog output to increase light/sound intensity.

From what I've read the only way to get that high frequency is to use port manipulation, but nothing I've found has mentioned multitasking while outputting a high frequency. If there is no way these three tasks can be done in unison then I guess I'll just have to use an external circuit to provide the signal.

Thanks for any help you can provide, and sorry for my lack of knowledge.