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I'm working on a 1993 Mercury Capri with the Mazda B6D engine. I had to replace the timing belt along with a few other things. I aligned the cam gears and the crank gear to the marks in these pictures but the engine still does not seem to run right, i.e., prone to shutting off, unburnt fuel, and a rough idle. After talking to the owner/driver of the car I found out that she had been having to slightly depress the gas pedal at a stop to prevent the engine from shutting off. She also recalled someone mentioning the distributor to her as needing to be replaced, although I'm not sure how reliable that information is. However, based upon what she said about her preventative actions to keep the engine from shutting off, I raised the idle to the point to where it idles around 1000 rpm, which I'm guessing is probably closer to what it should be than 600 rpm. However, the idle is still somewhat rough and there is still a significant amount of unburnt fuel. Does it sound like to anyone that I still haven't aligned the gears right, or is it more likely something else, such as the distributor?

If your timing was off your engine would run like p00p. My B6 ran so rich before I swapped I still have black exhaust tips.
Id suggest searching for how to's for adjusting the TPS, idle and perhaps replace the 02 sensor if your not sure when it
was last replaced. Also try running a range hotter for the sparkplugs, I never tried that maybe it will improve the burn.
You can also try timing to 12-14 degrees advanced up from the factory suggested 11 plus or minus 1.

Check for exhaust leaks in the rubber intake tube if its stock still, thats a big source of idle wonkyness.

Tried compression testing? Maybe bad valves? Thats further down the list, though... check simpler things first.

If I remember correctly, those are the timing marks for the BP engine not the B6.

Try page 85 in the online shop manual, the timing marks for the B6 are shown there.
It's not easy to read, but the E on the intake cam should match the E on the engine, and the I on the exhaust cam should match the I on the engine.

Yeah that's the BP diagram, to line up the B6DE's cams you line up the intake mark on the intake cam with the exhaust mark on the exhaust cam. Then bring the first piston to TDC and line up the distributor.