About multi-drop buses:
10 Mbit/s Ethernet, PCI and PATA are examples of multi-drop buses. They originally ran at 10 MHz (Ethernet) or 33 MHz (PCI, and intermediate versions of PATA). Enhanced versions have gone up to 66 MHz (PCI) and even 133 MHz (PATA with the special 80 pin ribbon cable). In the PCI case, it's all within the same PCB, which makes things a lot easier. PATA uses a ribbon cable. So in theory, if they can do that, you can do it too. However I suspect that some black magic is involved, I personally wouldn't vouch for a multi-drop bus running over any kind of cable at more than 10 MHz. But, remember this is MULTI-DROP. If you go to point-to-point links, the rules change.
100 Mbit/s Ethernet, PCIE and SATA are examples of point-to-point buses. By using a point-to-point link, you have much better control over the inductance of the link and issues like termination and reflection. This is good for 100 MHz without significant problems, even several Gbit/s if special techniques are used. However, note that you should really use dedicated transceivers for this kind of thing, if you just took a 74AC gate and tried to send 100 MHz data over it with a long cable, it would be problematic for a number of reasons. Noise pickup, ground issues, etc. So you should definitely be going differential, and preferably it should be isolated, as in Ethernet.
Now with that background, considering your problem, it would be 100% easier and better to have a separate connection or connections from your FPGA to each converter level. You've specified 100 MHz, and this just won't work well over a shared cable. Even if you used special transceivers and cables to make it work, there is also the problem of the connector, which is always going to add a lot of stray impedances, and a loose connector could bring the whole system down. If there are wiring considerations that make the single cable approach unavoidable, the best I could suggest would be a daisy-chain, that is, a series of point-to-point links (repeaters) from each level to the next.
Another way to do the multi-drop bus (if it absolutely must be a multi-drop bus) would be to put everything on the same PCB: the DSP, the FPGA, and the 30 levels. It would be a big PCB but quite workable. If you have a multi-drop bus WITHIN the same PCB, then with good layout techniques you could make it work up to 100 MHz. However, there'd be no point because the PCB would allow a star topology just as easily as the multi-drop bus.
So clearly the right thing to do is a star topology: reserve a couple of FPGA pins for communicating with each converter level, and have a big bundle of wires going to the level PCBs. Given that modern FPGAs have hundreds of pins, it would not place significant limitations on your design. And, the data rate would be so much reduced (kbit/s not Mbit/s), that no special techniques would be required, you could just connect the FPGA pins directly to the cable with say a 1k resistor and potentially a couble of diodes (one to each rail) for protection.
About isolation:
Isolated ADCs are going to be very expensive. Isolated PWM output slightly less so, since in general the high side driver needs to be isolated anyway, but even so, it would be much easier to put the isolation in between the micro and the FPGA, rather than between the micro and the PWM + ADC. A good way to isolate the communication between FPGA and micro would be to do it like the old MIDI standard: an opto-isolator is placed on the receiving PCB, and the sending PCB gets a pair of wires connected to the opto, which it can use to turn on the LED of the opto. (The opto can also be placed on the sending PCB and the open-collector output sent along the wire to the receiving PCB).
Another approach might be to use fibre-optics instead of wires. So basically the LED is on the sending PCB and the receiver (light detector) is on the receiving PCB. Look up S/PDIF with TOSLINK connectors for an example of this in practice.
Also, the micro could possibly be deleted if you use the right ADC. Certain kinds of ADC only require a clock input, and will regularly initiate a conversion and clock out the results. For example, many audio ADCs work like this, and can send the results in S/PDIF over a TOSLINK connector. I don't suggest to use an audio ADC as such, because they often can't handle DC and you need to measure the DC, but I am sure that an appropriate ADC could be found. If the conversions need to be synchronized, you'd need an extra opto (or fibre-optic cable) to distribute the conversion clock. As to the PWM, how about having one opto (or fibre-optic cable) for the low side and another for the high side, it has the advantage of simplicity and that the FPGA can generate the needed dead time, but may be unsafe as both can be turned on simultaneously. Or possibly just have an opto letting the FPGA drive the low side, and generate the high side with appropriate dead time locally based on what you see at the low side.
cheers, Nick