The Warp Engine 3040 looks like an excellent choice. Great SCSI chip and apparently a fast memory interface. I wouldn't mind an MK3, maybe even an MK2 - and deal with motherboard SCSI, which honestly isn't too terrible. For what it'll be used for, I'd be content with a nice '040 card. The educational software is a good idea... might be more productive for the kids than WHDLoad (LOL).
The MK2 is a real nice choice, I ran one for awhile with the MB SCSI. For the amount of data your pulling with an Amiga, it is more than enough. If you can find a MK3 or 3040, it would be the icing on the cake. I never ran a MK3 but I heard it fits perfect.
Sad story, I gave educational software as a gift, before I had kids. My relative destroyed all of them. I could recovery anything. A real kind soul recently sold me a nice collection and my kids are having a ball.
Not yet - I have yet to use (let alone obtain) the PhonePak. I never gave it serious thought until you mentioned it. It looks awesome! I noticed this note at amiga.resouce:
The phonepak really is SO nice. Compared to any phone system I have used, it is the best solution I have used. I may have a line on a card, I will make some calls and see if I can dig one up for you...
Did you experience this issue? My understanding was that this shouldn't be a problem with a Buster 9 or 11, or anything other than an early 3640 WRT the A4K.
Not an issue for me at all, with the Buster 11. I have no experience with the Buster 9 though. That was well documented by GVP years ago, you did need a z2 memory card if your buster could handle it.
So far, just the usual bits. Buster 11, DMAC 4/Ramsey 7, the upgraded WD chip, and a load of ZIPs to finish populating the motherboard. These were all a very generous gift from a good friend and fellow Amiga nut a few years back. I have an Ariadne and PIV set aside, though I might end up going with a CV64 - seems a shame not to make use of Amber. (There's the old Spectrum 28/24 I've considered using, a decent enough card IMHO.) Being left on for long periods, I'll probably re-cap the PSU and use some kind of HD surge protection. Aside from that, I'm trying not to get too carried away as I often do. I'm sure you know how that goes... 
Very nice system you will be building. Have fun.. It does start to eat up some time, because of the nostalgic fun... If you need anything to complete a system let me know what you may need, maybe we can trade or I may sell. I will be selling off one of my 3k's with a retina z2 and x-surf nic.
