Well, I'm about to finally upgrade the stock speakers, 2 4X6 in the front and 2 4X6 in the rear. Yes, that's right, they are all identical in my 380SE!
I read a number of good articles here, the most recent in the thread below ("W126 question for Scott"), showing the Eclipse Euro units favored by Scott at La Jolla Audio. (these are, I believe, part number ES-8462E, or ES-8463E. I'm not sure if the ones I list are the same)
Here are my choices, and I'm open to opinions on sound quality versus the $$ spent. I plan to run these off a Blaupunkt CD receiver.
MB Quart DKD 146 4x6 big $
Eclipse 84641E 4X6 big $
PIONEER TS-A4667 4X6 little $
PIONEER TS-G4647 4X6 little $
I measured up the openings, and it looks like any nominally-sized 4 X 6 should fit, as long as the depth isn't over 1 3/4" and the short-distance across the oval isn't over 3".

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1986 560SL
2002 Toyota Camry
1993 Lexus

i have the same setup that you have, 4x6's all around....right now i have some Alpine type S in the front and the MB Quart DKD146's in the rear...i like the Quarts the best, they seem to have a little lower bass response than the Alpines, but i like them both a lot... if i were you, i would just get some from ebay, either set will only run you around $40 and sound the same as the ones you'd pay $119 for in a retail store

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1985 300SD 192,000miles...Astral silver/ Grey MbTex

1983 300D 194,000miles...White/Tan MbTex...my newest addiction

Well, I found a pair of Sony's locally, marked down from $149.00 to $45.00, CDN. I also won a pair of Eclipse on EBay for about $60.00 USD, shipped.
I removed the package tray and used a jigsaw to enlarge the holes so the Sonys are a nice tight press in fit, and the grilles fit perfectly as before. I also replaced the disintegrated cloth with fresh material. I used a light contact cement spray to attach it.
I'm informed that the Eclipse are very high quality, and should drop right in the dash openings if I trim one ear off. They should be here in a week or so.

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1986 560SL
2002 Toyota Camry
1993 Lexus

i did that to my car too with the speaker cloth in the front...it made a hell of a difference, the original stuff was dry rotted and brittle and looked really bad...the only stuff i could find was Stinger speaker cloth and it ran me a little over 20 bucks for a piece about 36"x66"....expensive, but well worth it for the improvement in looks to me....i also used some to cover the 2 ports i made in my rear shelf to let my bass come through into the cabin, but that was kind of excessive and i regret it now...oh well

btw, don...whats the model number for the Sony's you picked up?...id like to see what 4x6 speaker costs $149...seems like you got a good deal on them....youre gonna be amazed at the difference in sound from the old crappy Becker radio and whatever kind of worthless speakers Mercedes put in there

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1985 300SD 192,000miles...Astral silver/ Grey MbTex

1983 300D 194,000miles...White/Tan MbTex...my newest addiction

They are Sony XS-4624. The $149.00 is CDN, and I've seen them on the net for $99.00 USD, so that's about right if you add shipping and exchange.
When it gets here, I'll be replacing my Blaupunkt Denver CD147 with a Blaupunkt Tokyo RDM169, and adding the 5 disc changer Blaupunkt IDC 09. The changer will be built into a custom box to fit the console, so I can change discs right in the driver seat.
Yes, I'm with you on the 350SE's package shelf. The 2 openings for the plastic trays vent nicely into the trunk, actually about 1/2 the area of each tray is entirely open (gas tank is under the other half), so no real need to cut anything out. Until I actually looked under the shelf from the trunk, where you can see the exposed bottoms of the trays, you don't realize that there is no real metal barrier on this model at all.
Other posters have had to cut openings as you did for other models of the 126 though, but until now, I didn't realize why my trunk mounted sub is so bass-rich in the cabin. Acoustically, IMO, 1/4" of hardboard (the tray lids) and 1/8" of plastic (tray bottoms) present no barrier to bass transfer at all.

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1986 560SL
2002 Toyota Camry
1993 Lexus