I can offer a few thoughts. First, I have 2 Eheim Pro II 2026s. They are rated for 53-90 gal tanks (200 - 350 liters). The larger 2028 is rated for tanks up to about 160 gals (600 liters). I think the 2028 is way overkill for that tank. If you did the 2026 it would be plenty of both filtration and flow for a 96L tank.
You can also basically create a river flow using a canister since you can place the spraybar across the side at one and and then your sponged intake system along the opposite side without needing all the pvc plumbing. You can gang two FilterMax III Prefilters for the intake.

These are aout 6 inches long and use an internal skeleton similar to the Hydro Sponges. The plastic adapter pieces come apart and interconnect to allow many configurations with a variety of connections.
If you are planning to start with closer to adult size fish then flow in the tank will be an issue. However, if you are starting with smaller zebras, then flow is not as much of an issue which means you can use a much greater variety of filters etc. Neither of my growout tanks has a powerhead, One has a sponge filter and small powerfilter and the other a pair of power filters.
Second, I am not a fan of heaters built into the filter for a few reasons. Only that specific heater can be used. If it breaks, you will need to have adequate backup heat in the form of a spare Eheim heater of other normal heaters. Also, if you have a heater in a filter, that means you have less media space avalable. I also use two heaters in all my zebra tanks. No way I trust my guys to a single heater which could fail. I do have an inline heater for each of my Eheims- they are placed on the return side of the filter and come in 200w and 300w.
Third, the choice of substrate type or going bare bottom is more an issue of personal esthetics. It is easier to keep a bare bottom clean that substrate which will suck in some wastes. I have both and the fish don't care. My personal belief is that the type of cover you provide is far more important. If you read the site link on the zebras natural habitat you will find the following paragraph:
The floor of the xingu is primerily made up of rounded rocks, crevises and a sandy substrate, allowing the hypancistrus zebra to travel throughout it's territory under cover from preditors.
Hence the saying here that a happy zebra is a hiding zebra. Providing appropriate cover is improtant to having happy and ultimately spawning zebras. Fry need smaller nooks and crannies than adults who want more room. Its is amazing to see how in a tank with 15 fry, almost all of them will try to hang together in a spot too small for anything else to fit no matter how many good spots there are. Here is a pic of the type of rounder rocks I use in my breeder tank. (Note this pic is to show the rocks and is not a zebra tank). I got the rocks at a local stone and gravel yard.
For fry I actually make temporary hiding places using smaller pieces of slate to support bigger ones. As many as 15 fry have camped under the one on the right and even more under the one on the left. When its time to remove/move fry. I can lift off the top pieces and then pick up the end supports. You will learn over time that catching zebra fry can be a challenge as long as there is one place they can hide under or behnd
I hope some of this is helpful but please bear in mind this is how I do things and is by no means the only way.