Physical Installation queries...
Dear Jim,
In order of appearance:
(My experience only, YMMV, yada yada yada, you know the drill...)
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1. Above the motor there is enough room for both the decoder and the keep alive,
Not for a commercial KA in my experience. That said, I have taken to building my own KAs using SMD Tantalum caps per https://model-railroad-hobbyist.com/magazine/running-extra/2018-12/stay-alive-n
and one additional benefit is that it allows the modeller to configure the physical shape of the KA as required.
In this case, building a "thin flat" KA to lie-flat above the decoder would-be entirely do-able.
For Ath GPs, fitting the KA above the decoder, up in the forward air-cleaner/dynamic area (just behind the cab) , as opposed to directly-over-the-motor, is a common option.
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2. Is there any problem in mounting one on top of the other?
(KA on top of decoder, or vice-versa)
Not as long as they are appropriately insulated (heatshrink, kapton tape, etc), and you have confirmed there is internal room within the shell at that point.
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3.The copper piece above the motor carries the power to the + side via a spring that connects to the brush. Can the decoder and keep live be mounted right on top of that copper strip?
I have mounted fully-heatshrinked decoders (Think SoundTraxx Tsunami) directly on top of the Ath motor before, with Kapton tape holding it down, BUT as extra layer of kapton tape is never a bad idea... 
...and I would NOT "direct mount" any form of "bare circuitboard" decoder, like a SoundTraxx "AT", "KT", or "21-pin", any TCS, or any ESU decoder that way... (see below)
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4. Is there any reason I cannot put a piece of kaptan tape across the top of the decoder and keepalive and down the two sides of the motor ?
Assuming you have the appropriate insulation between the copper strip and the decoder/KA stack-up, sure, an "inverted U" of kapton tape from one side of the Ath "gold side" motor, up over the decoder/KA, and down the other side, can work fine.
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5.The 4 arrows are pointing to plastic stubs that are just a little higher than the copper piece. Would it be better to glue a piece of styrene across the top (of the copper clip) and attach the decoder to it - with glue? With tape?
If you get a strip of styrene which is just-so-narrower than the stubs, so it sits down nicely in the "trough" above the copper clip, (IE sits along the linear centreline of the mech)
kapton-tape it down (motor side> over styrene strip> motor side)
then lay the decoder/KA stack on top of the styrene strip,
and do a 2nd "inverted U" of kapton tape to hold the decoder/KA,
you can have the whole thing "buttoned down" quickly, and yet still have it "completely reversible" if required...
Alternatively, a smear of Aileen's Tacky Glue, neutral-cure silicon, or similar would also work to hold the styrene strip down... (IE a glue which will "hold on", but can be peeled-away if required, and does NOT promote corrosion of the copper plate or surrounding metal components...)
NOTE! Given you will need to solder the ORANGE "Motor +ve" wire to that top copper clip, make sure that the styrene strip allows space for that wire-feed and solder-joint (blob?)... lest you try to mount the styrene and then have to remove it to solder the wire, OR mount the styrene after soldering the wire, and can't work out why the goshdang strip of styeren won't sit flat accross the top of the motor...
(we've all been there...)
Just a side-note, on my installs, I tend to use a strip which is _longer_ than the motor, and overhangs the rear-truck driveline at-the-least, and sometimes the front truck too. This occasionally allows me to mount the decoder "in free space" over the rear truck, and use a thin iPhone speaker mounted above the motor. Sounds crazy, but it puts the speaker where the exhaust, IE the actual "point of noisemaker" actually is, mid-way along the long-hood, making for (IMHO) a sligtly better overall impression on near-eye-level shelf layouts and similar
(IE when the loco is up closer to your head, IE where your _ears_ are... ).
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6. The speaker to the right will fit above the flywheel housing, which has a rounded top. Can the speaker just be glued to it? With what glue? Or double sided tape?
Or do I need to create a little table top on top of the housing and tape or glue to it?
That "curved housing" covers the rear truck worm, and swivels L<> R as the truck moves around corners. Ergo no, mounting the speaker (or anything really) to this is not a good idea. Better to somehow suspend the speaker over the rear truck, so it's mechanially clear of the drive and worm/gear-tower. Many modellers mount the speaker up in the rear roof-area of the shell, as there's a lot of space up there in Ath geeps. As above, I try and mount the speaker further forward for audio-performance reasons, but that "styrene strip" extended rearward from the motor can work great as a "suspended platform" on which to kapton-tape the speaker, or decoder, as you feel soo led....
...speaking of LEDs, by suspending something in that space above the rear truck geartower, you are also creating a platform which can hold a 3mm LED in the perfect position to shine thru the rear headlight holes, once the shell is sitting-down in position. (This speakes to the concept of doing the install with all active stuff mounted "on the mech/frame", and minimising the wiring/connectors that need to join the mech and the shell...)
Now, you could put vertical styrene legs directly behind the motor, and in the rear-corners of the hood,
glue a sheet of styrene on them and thus form a platform which is the full-width of the hood, but I find the single-styrene-strip technique simpler and faster. I'm sure someone has looked at this and thought "I could design a drop-on 3D print rear-platform for mounting stuff above the rear truck geartower", but by the time they've had that thought, I've already kapton'd on a length of styrene (or stripwood, or....) and moved-on with the install...
I hope this helps. We often think of onboard installs with a focus on the wiring (resistor values, SMD or 3mm LEDs, etc) and programming, but the sheer "how do you make it all fit?" physical installation details and factors are very fundamental and relevant to a successful deployment that runs troublefree...
Happy Modelling,
Aim to Improve,
Prof Klyzlr
