Yeah I think the PS3 has an internal storage limit of 2tb and I think the highest drive it can work with is under 4tb? Would need to do some digging to confirm that, it's been a while since I did mine.
What's the serial number on your ps3? The noise could be related however it could also just be a coincidence.
Just for the sake of ruling it out, does webMAN MOD/sMAN crash/freeze when you don't have an external drive connected? If it works with out then it's having issues with that enclosure. It's kind of a long shot but a good starting point.
Now if that doesn't change anything try different releases of webMAN and sMAN, it's possible the versions you're using are at the root of that problem.
And last but not least, the multiple package issue leaves me thinking again that it has something to do with the external drive being used. If possible try a usb flash drive and try smaller size packages and see if that helps. I keep re-reading your original post and all of the issues leave me thinking the problems are all due to the external drive and it's enclosure...
My PS3 ISO games running from an external HDD randomly hang for a second or not even that and then return to normal. This happens sometimes.
I'm almost 100% certain that the your external isn't able to keep up with the rest of the PS3 and it's stuck waiting for the external to provide the data it needs.
Most external drives are meant to be used as storage (ex. Backing up pictures/videos/documents) so they come with a controller (the chip that does the communications from the drive to the usb) that isn't ideal for running steady streams of data from (some have a dedicated power supply others rely on a second usb cable to power them)
The HDD inside the enclosure is also going to follow the same line of design. They get a smaller cache, slower read/writes and random/sequential performance as it's not necessary if your just moving files back and forth.
Now your 2.5" drive that you had for your PS3's internal storage has some major benefits. Right off the bat you ditching a man in the middle and going from the drive right to the PS3's own storage controller. It's got it's own dedicated power supply, so none of this power saving bullshit we have no use of in this case. But most importantly, your probably working with a higher performing drive that has a bigger cache, better read/write times and much better random/sequential performance.
If you can get me the make and model of your external drive and I'll be able to rule some stuff out.
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