Hello everyone! I've searched around the forums a bit and couldn't really find an answer so I'm going some of you can help me figure this out.

I have a 1990 240DL, 230,000, standard transmission and I love her dearly. However, she's been a little difficult lately.
The idle is a bit low and rough and seems like it wants to stall (but hasn't yet) and when I give it too much throttle too quickly, she chokes up and jerks until I ease off a bit. If I completely floor it, there's power loss and the car slows down until I once again ease off the gas. I've also noticed that when shifting gear and switching off between the clutch and gas pedal, it sounds like it's missing. Just one single 'poof', but its there. It seems to be missing a little during acceleration too but I can't really hear it.
I checked the trouble codes (CEL is on) and got 1-2-1 and 1-3-1. The maf was just replaced a couple months ago and didn't seem to fix the problem. The car also has new distributor cap, rotor, and wires as of a year and a half ago.
Also, with code 1-3-1 which is "RPM sensor to EZK missing", it doesn't match the given symptoms which is the engine not starting. The car runs fine otherwise, and as long as the acceleration isn't too fierce I've had no other problems. However I want to fix it so it's not constantly in limp home mode!

I did just recently noticed that it has a small exhaust leak further down the pipe before the muffler, but I couldn't detect one close enough to the engine where I think that could be the problem. I used to have a Hyundai that exhibited the same problems as the 240 so I replaced plugs and wires and distributor, which helped slightly, but it turns out there was a hole in the flex pipe causing the loss of power and misfiring. Do you think the exhaust could still be the problem? I'm at a loss.

Edit: I forgot to mention, when I have the key in the 'II' position, I can hear one of the fuel pumps turn on, and it stays on. Is this normal? If I'm under the hood, I can hear it near the fuel pressure regulator. However, there doesn't seem to be any leaking of any sort. I thought maybe the pre-pump could be one of the suspects in the hesitation.