Hi Marcus,
well done for your post and pics on the wiring, that certainly helped. The guys have got you pretty much sorted out.
There is no need to give up on that internal wiring, remember one of your initial BT Speedtest results was from MS2 with a sync speed of 7616. Just to confirm you should have disconnected both the orange & the white/orange wires at MS1 and MS2 leaving only the blue & white/blue wires connected as pointed out by Santiago. There is no need to worry about disconnecting those orange ones at the connection boxes.
Frankly you were lucky, only by the use of filters, that any phones worked/rang, as the connection of those orange wires to the terminals they were on, on the MS2 plate, would have resulted in the main bell capacitor in MS1 being shorted out! At least the dodgy electrician managed to keep a genuine BT Master socket at MS1, so you won't get into any trouble with BT.
There is the possibilty that the filter you were using when you were testing at MS1 in the Test socket is faulty, if it was the same one you normally use at MS2. If it was a different one, then it could be the router as has been suggested, so trying a known good one will eliminate or prove that.
Once you have the router issue resolved, you can try some more tests. Personally, I'm not so sure I like the look of the quality of the 'Filtered Socket' FS - does it have any identifying marks or brand names?
If it can't be establish to be a high quality plate meeting BT spec.sin 346 v2.2 or higher, then I think I would replace it - with either - a standard secondary socket and a plug-in high quality filter, or preferably - a high quality filtered extension plate as supplied by 'adsl nation' or 'clarity' because you are using a DECT phone as well as an answer phone. (Personally I would also replace MS2 with a high quality ADSL filtered extension plate, but wait and see what results you get once the fault is resolved).
Let us know how you get on with the filter and router checks.
