OK, so it sounds like it's a given that:
* One of the MAC radios will be replaced by a GTN 650
* KMA-24 audio panel will be replaced with a Garmin (I recommend the GMA 350c so you can talk to the GTN - Makes it much easier and faster to get around the GTN)
* Century IIb will be replaced with a GFC 500
* KT76A will be replaced with something new
* G5 will be the standby.
It kind of already sounds like you've decided on Garmin. The G5 isn't approved as a backup for anything besides the Gx00 TXi - The backup for the certified Dynon SkyView HDX is the Dynon D10A. While I'm not sure that's stipulated in Dynon's STC, I do know that the G5 itself isn't approved as a backup instrument except as part of the STC for the TXi.
Also, the GFC 500 requires the G5, it's an integral part of the system. So, you can't do a GFC 500 with Dynon unless you have the Dynon panel (primary), an approved backup (Dynon or otherwise, but not G5), AND a G5.
Now, if you just want "something like a G5" and "something like a GFC 500" then there's a conversation to be had, because Dynon has an autopilot that I think is just as capable as the GFC 500.
If you have the flexibility to go with Dynon as opposed to specifically having the G5/GFC 500 combo, you can get pretty much everything from Dynon except your GPS navigator, for which you can still get the GTN 650. So, you could have:
Dynon SkyView HDX STC $2000
Dynon SkyView HDX "Basic Package" (10" display, D10A backup, and associated hardware): $9465
Dynon ADS-B In/Out: $3163
Dynon autopilot: $2808
Dynon engine monitoring: $1637
Dynon interfacing hardware: $863
Garmin GTN 650: $11,995
PS Engineering PMA450B: $2,595
Total equipment cost for SkyView HDX panel: $34,526
Looking at the Garmin side of things, it looks more like this:
G500 TXi, 10" display: $15,995
G5 AI for backup/AP: $2249
GTX 345: $4995
GFC 500: $6995
GTN 650: $11,995
GMA 350c: $2395
Total equipment cost for Garmin: $44,624
Now, these are retail prices and don't include installation, which is going to be significant. Now, you probably won't pay full retail on the Garmin stuff since there are package deals, Garmin "Seminar Bucks", show deals, etc. I'm not sure what sort of discounts you can get for Dynon.
Installation-wise, Dynon claims theirs will be easier to install, which is likely true - They're used to selling their stuff to people who have never installed any avionics before, so a lot of things are pre-wired and generally made as easy as possible to begin with.
Either way, getting all this done within a $40K budget is going to be difficult. For reference, we installed a GTN 750, GTX 345, GMA 350c, and FlightStream 510 in late 2017. Our retail equipment cost would be $26,380. Total installed cost including dealer discounts and $600 worth of Garmin Bucks, $1100 rebate from Garmin and $500 from the feds was $36,085.50, so figure the labor cost was in the neighborhood of $10,000. Subtract the $5500 price difference for the GTN 650 instead of 750 and it'd have been $30,585, and that's without any glass or new autopilot and the additional labor associated with those. Do the whole thing and I'd expect you'll be in the neighborhood of $15-20K for labor, pushing your cost up to maybe $50-65K total.
@Jesse Saint, am I in the neighborhood here?
Of course, there will be additional costs - The good old "While we're in there" stuff that makes sense to do now instead of later. We pulled out a bunch of old stuff, replaced a bunch of coax and a bum com antenna, refurbished the KX-165 Nav/Com radio that we kept, replaced the shock mounts on the panel, replaced a bunch of lights and filters, overhauled the turn coordinator, adjusted and calibrated the autopilot, etc... All that "while we're in there" stuff cost another $5.2K.
We did go with a really good shop instead of a cheap shop, but cheap ain't cheap in the long run. We may have paid some for quality, but the job was done on time, on budget, and everything worked perfectly with the stuff that was still in the plane, right out of the gate. Haven't been back to the avionics shop at all in the ensuing 15 months.
Bottom line, your decision may be driven by budget as much as anything else, and I would recommend a quote from one of the Dynon shops like Sarasota who has done plenty of installs on both systems to see how much the installation will affect things.