The ML systems in these trucks are garbage. In fact everything Lexus did in the early 2000s after Nakamichi (which were probably the best factory systems of the time) left the business is trash. It took several years for the systems to become worthwhile again in my opinion. JBL and ML are just different spokes of the Harman empire which is now owned by Samsung. However, if you choose to repair versus replace these ML components, be aware that unless there has been some dramatic improvement in foam technology, if the refoam kits you're receiving are actually just more foam and not butyl rubber surrounds, you're going to be tackling this problem again in another 10 years or so depending on your climate. And you still just have a marginal ML system. I'm usually a VERY ardent "keep the system stock" proponent, to the point that I don't actually mind the old touchscreen Nav radios as much as so many here do, but when it comes to the component parts of the system itself replacement is worth the effort.
Everyone is entitled to their opinion, but for anyone reading this thread, please don't immediately take the post I quoted as fact. The Simply Speaker replacement surrounds are NOT foam, and will last a very long time.
To an earlier poster re/ disintegrating foam being a cause of poor sound.. The foam surround's two main purposes are to keep the voice coil centered so that it moves freely around the speaker magnet, which in turn moves the cone, which is what moves the air and creates sound. The foam also acts like a damping mechanism, similar to a shock absorber. It doesn't have anything directly to do w/ sound quality, but when it disintegrates the voice coil rubs against the magnet impeding motion, and the speaker also goes past it's design excursion parameters... like bottoming out when your shocks completely give up the ghost. Both of these things cause the buzzing and distortion you're hearing. Replacing that surround foam is a simple, easy process and will return your speakers to as-new performance, provided the voice coils aren't burnt out (and they probably are NOT... they're most likely fine).
Now, regarding the opinion stated above about the "garbage" status of the ML system. I could not disagree more strongly. If you're looking for body-shaking, mind-numbing bass that'll shake the other cars off the road, or ear-bleed-inducing screechy treble like most of the car audio systems I've heard, then yes, you may not like the ML system. However, if you listen to acoustic music, or any type of music where fidelity to the source is important to you, then the ML system is one of the best out there. My wife and I are both professional musicians, and her ONLY criteria for her next car is that it, too, has the ML system in it.
Sooo... like I said, everyone has opinions, and are definitely entitled to them. Form your own... fix your ML system and decide for yourself. I doubt VERY much that you'll consider it garbage, and I'm fairly sure you will appreciate it a great deal... and increasingly the more you listen.
Edit.. To be honest, the more I think about the post I quoted above, the more bugged I get. Audio (not specifically car audio, but speaker design, recording, sound reproduction, etc) is one of my areas of a certain amount of expertise, and when I see something as blatantly wrong posted like that in what seems to be a helpful, well-meaning, articulate manner, I become concerned about the things that I DON'T know anything about but come here asking for help. Suppose I asked for some hints as to what gas to use in my LX470 and some articulate, very confident person advised me to use E85 or diesel only, that regular Sunoco gas would ruin my engine, and I should stick with 20w50 in the engine. Obviously, that's an extreme example, but seriously... I'm all for people having opinions, likes/dislikes, and even being proud and defensive of their choices, but if you're going to make a statement that the ML system is garbage and that you're going to improve it by swapping out the speakers, at LEAST say "I think the system sounds awful and here's why" rather than label it as garbage. Yours might sound awful because there's something very wrong with it, not because it's garbage. Or.. it might sound awful simply because you don't like accurate audio reproduction. That is your right. BUT... to advise others to blindly follow you is just not a kind thing to do. Of course, it's the internet... reader beware, caveat emptor, and all that stuff. No one should ever blindly follow ANYONE on the internet, and should read and research enough to be able to tell the wheat from the chaff.