Doc B answered most of these; I'll just touch on a few output transformer points.
The power transformer is a proprietary design with several features specific to this amplifier. Among other things, it operates at unusually low flux density, and the windings are arranged to shield each other, and to shield the internal voltages from the external circuit. These features were chosen to reduce electric, magnetic, and mechanical sources of hum, buzz, and power line noise.
The Magnequest page shows upgrade kits, consisting of two output transformers and two plate chokes. The Paramour kits include the BH-6 plate choke; the Paramount kits include the larger BH-7 choke at the cost of $50 more. Both have the BH-5 output transformer, and you have a choice of core materials. The BH-6 is rated 50mA, which is fine unless your power line is too high a voltage - above 240v (or 120v if you have that power transformer). A high line voltage will also increase the 2A3 current, in which case I would get the BH-7s. But consult with Mike at Magnequest about getting BH-7 chokes with a slightly smaller air gap; it might be worthwhile and he is sometimes accommodating about such things.
There is one other option. You could get a full TFA-2004 - like Doc B, I prefer the Permalloy core. This is a true classic transformer design, possibly the best I have ever heard - the TFA-2004Jr and the BH-5 use the same coil geometry on a smaller lamination stack. It must go on top of the chassis; it just fits but you would have to drill appropriate mounting holes and an entry hole for the leads. The thicker core gives greater magnetic headroom (cleaner, deeper bass - in theory at least). Personally, I think that is not cost-effective unless you are using the 300B, but you asked for full disclosure! The larger core might reduce the treble extension in theory, but I haven't made enough detailed measurements to be sure of that since the insulation materials are different.
I have not done any direct comparisons of silver vs. copper wire so I can't comment. It would surprise me greatly if any such differences were more than a tiny fraction of the core material difference - but I've been surprised before and expect I will be again. :^)
The BH-5 and Jr coils have taps at 8 and 16 ohms; the full-size TFA-2004 also has a 4-ohm tap. The stock Paramount transformer can be wired for 4, 8, or 16 ohms but they are not taps - the secondaries are connected differently to obtain these impedances, either with soldered connections or with a 2-pole 3-throw switch (not supplied with the kit).