Tap your cats with a rubber mallet. If they rattle, they are probably due (overdue at that mileage) for replacement. A clogged cat will cause misfires.

Have you read for pending codes?

 

You should do a search. Been talked about a lot.
However, the most likely failures are 1) a crankcase vent valve, 2) an intake leak (boot, vacuum line, etc), and/or 3) low fuel pressure.
It's unlikely to be a cat converter. However, constant lean running can damage them, so fix it quickly.

Cars don't run lean due to spark plugs. They can misfire, but they will not cause the lean condition. The Misfires are gonna be due to the lean condition, not the cause of it.

 

getting codes P0171 and P0174 (lean mixture) and P1342, P1344, and P1347 (misfire cylinders 1-3).

Very common. Very easy. Very hard. Depends on what it is.

I'm battling similar subtle (can't feel it) lean-mixture misfires myself:
- Does the order of the misfire OBDII DTCs diagnostic trouble codes actually matter (1)

I'm starting with the vacuum hoses, since my plugs are new, and my CCV tests OK - yet my hoses are crumbly & my VCG is leaking on the passenger side & I have 100K miles on my fuel pump, fuel filter, and fuel injectors (which have only burned lousy Costco regular gas in the past 8 years and which are often driven on near empty):
- How to locate all the vacuum hoses in the E39 engine bay (1) & where to get those vacuum hoses (1) & what sizes to get for all the M54 engine vacuum hoses (1) & correcting the F-connector errors in the realoem diagrams (1).

So far, the list of hoses to check seems to be the following:

Engine => Vacuum control => AIR PUMP F VACUUM CONTROL

• 04 VACUUM HOSE BLACK 3.3X1.8 11657803732 $16.43 (two pieces)
• 03 VACUUM PIPE 1 11727574490 $27.94 (one piece)
• 07 VACUUM HOSE BLACK 3.3X1.8 11657803732 $16.43 (two pieces)
• 09 VACUUM CAP (no part number shown)

Engine => Exhaust manifold => EMISSION CONTROL-AIR PUMP

05 PRESSURE HOSE ASSY 1 11721435456 $22.73
​

Fuel Preparation System => Fuel Supply => Fuel filter, pressure regulator

• 13 VACUUM HOSE BLACK 3,5X1,8 11727545323 $14.82
• 11 Hose 1 13321437801 $24.87

Engine => Vacuum control => Vacuum control - engine

• 02 Hose elbow 1 11617503666 $8.17
• 03 Hose elbow 1 11617547582 $17.25

Fuel Preparation System => Fuel injection system => FUEL TANK BREATHER VALVE

• 03 fuel tank breather line 1 13907557924 $27.77
• 04 fuel tank breather line 1 13907504303 $27.77

Engine => Cylinder Head => Crankcase-Ventilation/oil separator

• 02 Vent pipe 1 11611432559 $25.73
• 03 Connecting line 1 11617504535 $33.87
• 04 Vent hose 1 11157532649 $15.37
• 06 VACUUM HOSE BLACK 3,5X1,8 ? 11727545323 $14.82 (not on all E39s)
• 07 Return pipe 1 11617504536 $33.87

Of those above, these smaller hoses seem to be most problematic:

• 04 VACUUM HOSE BLACK 3.3X1.8 11657803732 $16.43 (two pieces)
• 07 VACUUM HOSE BLACK 3.3X1.8 11657803732 $16.43 (two pieces)
• 09 VACUUM CAP (no part number shown)
• 13 VACUUM HOSE BLACK 3,5X1,8 11727545323 $14.82
• 06 VACUUM HOSE BLACK 3,5X1,8 ? 11727545323 $14.82 (not on all E39s)

And, these larger hoses are apparently problematic:

• 02 Hose elbow 1 11617503666 $8.17
• 03 Hose elbow 1 11617547582 $17.25
• 02 Vent pipe 1 11611432559 $25.7303 Connecting line 1 11617504535 $33.87
• 04 Vent hose 1 11157532649 $15.37
• 07 Return pipe 1 11617504536 $33.87

I was going to replace in this order: spark plugs, then coils, then ???

Neither of which will make a bit of difference on a lean-mixture situation; but replacing the plugs at 100K miles is a good thing.
- BMW spark plug application charts (1) (2) & the best plug to use (1) (2) & a deciphering key (1) & keys to reading plugs (1) & the truth about torque & anti-seize (1) & the truth about gap (1) (2) & DIYs for replacing spark plugs (1) (2) (3) (4) (5) (6)

As for the coils, nobody sane replaces them willy nilly ... you test 'em first:
- How to test a BMW ignition coil (1) (2)

Should I change the plugs or do something else?

I'd go down this list:
- How to diagnose a BMW E39 engine misfire (1) & how to battle E39 vacuum leaks (1) (2) (3) & how to solve specific vacuum leak diagnostic trouble codes such as P0171, P0174, P0313 (1) & P0170, P0173 (1) & where to find all the vacuum hoses in the E39 (1)

No rough idle (hardly, after replacing the DISA valve). I drove it about 50 miles yesterday, is this super dangerous?

Is the yellow SES blinking?

Tap your cats with a rubber mallet. If they rattle, they are probably due (overdue at that mileage) for replacement. A clogged cat will cause misfires.

Hmmm.... I don't think 'this' is in the misfire thread (I'll look, and add it if it's not there currently).

However, I'm curious ... HOW would a cat cause a misfire? (And, particularly a lean condition misfire?)

most likely failures are 1) a crankcase vent valve, 2) an intake leak (boot, vacuum line, etc), and/or 3) low fuel pressure.

I borrowed the free loaner (with deposit) Autozone CP9220A which I hope to learn from but I haven't yet used it since I'm first working on the vacuum system before I move on to the fuel system (I have 90 days):
- While replacing your spark plugs (1), where is the fuel system pressure test Schrader valve for the I6 (1) and for the V8 (1) (2) (3)

BTW, this is a rarity, but nobody seems to know the answer to this vacuum hose question:
- For all to benefit, WHERE are the ends of these hoses in our beloved E39s anyway?

 

Wow, that's a really nice kit!