You have done your research! (Thank you - makes it easier)
The 40W versus 25W - you want to run 40W mode?
IF you do, this is why the Diode is in place.
Why Doesn't it affect SSB power?
Because of how the Diode - operating as a one way valve - does not allow nearly 1/2 of the audio power envelope to be used as a means to "sample and smooth" - think of this as an NPC mod, but you do this to the limiter.
Why does it affect SSB? Because of the Radio Design, the methods used to limit Audio envelope - uses the RF power knob - much like a Mic Gain, but it's not controlling Mic gain, your audio - just affecting (attenuating) the audio AFTER all the effects have been applied - to the RF signal now attenuated to a low level signal sample.
When you Run 40 watts, the ALC/AMC and any other limiter effect needs to be kept in proportion to the level of signal you wish to control - which is why I have to issue to you, that cautionary statement of shortened lifespan. A high SWR, poor power supply - and thermal considerations (Those Bipolars are not bulletproof) the hi-po setting will take it's toll on your system. They, didn't put that in like you'd see in Galaxy class radio chassis - like the 959
One on Left is Magnums' but FEEDS into it...not adjustable...in this method.
On the Right, Is Galaxy, using two methods directly applied.
Both "sample" and control envelope - one is done by MODE
the other is done by adjusting Drive thru knob directly.
In SSB mode, the above left option you HAVE to use Mic gain.
In SSB mode on the Right- you control the drive used to limit Power on the RF knob.
These methods are different per function as similar but wiring is different.
You just bought the thing - so why not run it safely for a least a day or two while you sort out the functions you wish to keep and others you may need to work on...read on...
So you either run the 25 Watts - and save the radio for your enjoyment - or run the radio in this Hi-Power Mode and possibly shorten the life of this radio - if you use the 1969 BIPOLAR finals - they don't make these as OEM's (Original Equipment Manufacturer Mitsubishi) so repair options become more limited to MOSFET replacements.
As far as the "red "squares" goes...
Not too worry, you're fine.
The metal Plate one protects and shields a specific "VCO and TUNING" area from noise that can affect its operation.
The Red squares are other SENSITIVE areas that need to be kept isolatedisolated from the rear case panels - potential shorts can occur in these areas that can ruin the radio - it is to prevent a vibration from the mobiles setups that can force the cover plates to be too close for clearance.
Note the lower right one is protecting the IF/TX RF strip and also has a shield plate for this same reason.