If you have your heart set on this, here are my two suggestions:
If you really intend to use this as a daily driver, get your modern system of choice. Something like Z97, or AM3+, as that's what will usually have some PCI. Get PCI (PCIe is even better) interfaces for what you want (IDE/SCSI) or even get something like AM2/AM2+ which will usually have IDE and SATA on board, as well as some more PCI slots.
Get some USB ISA slots. I'd not go nuts, as to make this truly useful, you won't be benefiting much from these. For graphics, get a GTX 7800 512MB, as these are dirt cheap (last I checked, I got two for 20 bucks a pop), and will be still able to do high resolution work. You will be dual booting your modern operating system of choice (Linux will actually not be a bad idea here, as you might even get drivers for some older cards, and things like USB ISA slots) and Windows 2000. Windows 2000 will very likely support much of your older ISA hardware, with USB ISA slots, but will still be able to hold up with some newer tech, like the 7800.
The other idea is to get the biggest, baddest Slot 1 configuration you can get. If you can find Socket 370 or Socket A boards with half PCI, half ISA, even better. Something like an SE440BX-2 will be perfect for you, as they are dirt dirt cheap. Get the fastest Slot 1 card you can find/afford, and stick it on in. You will now be getting two graphics cards. Get the fastest thing on PCI you can get, something from nVidia, as a few manufacturers made some semi-competent PCI graphics cards. Then, get an AGP card of your choice. GeForce 2MX isn't a bad choice here, it's what I have in my P3-450 machine, and it could afford to be in really any Slot 1 machine. If you want, you could in theory get an end of the line AGP card, but you might have some issues with link speeds, I don't know.
For an OS, you will be using 98SE, and ArchLinux x86 (or your choice of a barebones i686 Linux distro). Modern Windows will not work or be practical here, so you will have to rely on Linux to do your CAD work, if you can find a usable alternative to AutoCAD on it (who know, maybe it works on Wine, maybe there's even a Linux version). You won't be doing ANYTHING fancy here, as even a 1Ghz Pentium 3 won't be powering you hard, especially at high resolutions. Regardless, you should still be able to do some CAD work here, while having a machine that is right in the perfect position for much of the early Windows, late MS-DOS library. If you can get a Voodoo 3/4/5, that will make it even better, as you will have Glide support.
Neither of these are good options, and you will ALWAYS be making compromises, expensive purchases, and honestly a whole load of decisions that could easily be solved by just having two computers. Even getting something like an ATX super tower that can fit two motherboards (One full size, one mini-ITX) would work better here.
If you want to save space, I suggest to plot exactly where you want to be playing legacy PC games. If you are into earlier DOS stuff, a low power 386 or high power 286 will be your friend. Later DOS stuff is done well by anything from a 486 to a Pentium 3. Early Windows titles are good on anything from a 486 to a P3, with only later stuff like Half-Life needing Pentium 2/3 power.
I'd suggest a Pentium Pro machine, as they are very capable on most mid-late non-CPU locked DOS games, but can hold up to a LOT of 1998-2000 stresses, like Half-Life and Unreal, especially if you get something like a Voodoo 2, or comparable. Either way, I will leave the specifics to you. If you need help, I have some good experience making and building older PCs with the intent of having nice legacy rigs, so shoot me a PM, I can help you out.