in my experience having truly separate AGND and DGND nets almost never works out well in practice. 90% of the designs i see that try to do this end up with current loops that introduce EMI issues and can generate more noise in the analog portions of the circuit than using a single ground with careful part placement would.
Having two GND planes also creates a problem for routing in that signals referenced to a particular ground should only ever be run on layers that are adjacent to this plane or its associate power plane. This can result is a pretty funky stack up that can limit where you can run traces. Your best answer would be AGND,signal,?GND,POWER,signal,DGND but thats funky to layout, uses lots of vias, only gives 2 signal layers to route on.
What i would recommend is a single solid ground plane and careful part placement. High speed digital signals and noise will follow the path of least inductance to ground not the path of least resistance. The path of least inductance is the smallest loop area, for signals this is directly under the trace on the adjacent ground plane. In some cases a ground pour on top, bottom, or both can be helpful in reducing noise pick up as well. This is dependent on the components and the design layout.
Create virtual partitions, keep out areas, where you only run either analog or digital signals, keeping in mind that the return current path for the low frequency analog signals is the path of least resistance, while the return path for the high speed digital signals is the path of least inductance. As long as your careful to ensure that the return current paths don't cross, especially a digital return running under your analog sections. You shouldn't get much noise pick up at all.
If your have a particular device that is very sensitive to noise, such as a high resolution ADC, you can use a ground island to increase noise immunity, like this:
alt text http://www.hottconsultants.com/techtips/a-d%20gnd%20plane.gif
In cases where i have some sensitive analog circuitry i will usually also use a power island that is separated from the digital power supply by an LC filter of some sort, depending on the digital frequencies i'm wishing to block.
In answer to your questions,
Remove the third lead, this will let you clear/prepare the pads for re-soldering.
It's probably best to flick the old solder off the leads; do this by heating and bending the lead with the tip of the iron and letting it spring back, DO NOT DO THIS TOWARDS YOUR FACE!
You can buy solder with a flux core. Also, if you can get it, buy lead solder, it is MUCH nicer to work with.
As regards the vid:
Yes the guy tins his iron to remove the leads, you should always tin (add solder to your iron tip) before you do anything, it stops the tip oxidising. It also helps when melting old solder.
To clean the pads generally I would put a bit of new solder on, then wick it off to give a nice clean and shiny surface.
He is applying flux, this will stop the solder "balling up" and sticking to stuff it shouldn't. You can do this, but if you are careful, and have flux core solder, you wont need to.
As regards the rest of your questions, this is just about technique. The guy seems to tack solder (a connection made to hold it in place) the leads at first. When the whole lead is tack soldered he goes around and tidies up the job.
So what YOU need to do.
Remove the lead - Tin and clean the pads and flick the old solder off the end of the lead (NOT TOWARDS YOUR FACE!)
Add a little solder to each of the pads
Place each lead above the pad and push down gently whilst touching the tip of the iron to the solder you placed on the pad. Make sure you remove the iron before removing the pressure.
When all connections are made, get some tweezers and push down on each lead in turn, melting the solder on the pad with the tip of the iron so the lead is properly flat on the pad.
Remember! Before you touch the iron to anything, make sure you have applied some solder to it and wiped it off on a sponge.
Also, if you are buying new equipment, when you first turn the iron on, keep adding solder to the tip and wiping it off. You need to thoroughly tin/protect the tip before you start using it. You can get little pots of hard flux, this is useful and it will help remove the crud on the tip due to oxidation. Also, tin it and DON'T wipe it off when you are done, the tip will still be hot for a while after you switch it off.
Best Answer
Use a zero-ohm SMT resistor for the strap. The cost of the resistor is about as close to nothing as you can get (tenths of a penny, even on Digi-Key) and will be reliable. You call out which version by using a different bill of material (BOM) when you go to build the board.
Using a solder bridge would not be reliable, and will not pass DFM analysis at the manufacturing side. (They actually design their processes to avoid bridging.)
Even worse, you'd have to have different pastemasks which will far outweigh the cost of the resistors. A pastemask costs about $500 for a small board. For that, you can buy about 500,000 resistors.
The very cheapest way of all if you are fortunate enough to have extreme high volumes is to have a different PCB for each variant. You generally don't want to order more boards than you can consume within 3 months or so, as the boards will oxidize if they sit too long and thus have yield problems.
As far as layout concerns, for fullspeed USB you don't have significant SI issues that would be caused by such a jumper. Even USB highspeed would be just fine with the strap in series, though you'd need to pay more attention to stubs.