It has been said that as a small firm you spend most days hunting elk, but you usually end up eating squirrel. I would add the caviate (from experience) that you have to be careful when you catch an elk: They can kick a lot harder than a squirrel.
There are more issues to consider than has been flushed out in your email and many good questions have been raised. I would add that you need to consider the contract that you can negotiate carefully with respect to those things that you can not control. Chief among them are the management practices of your client (the architect) and more importantly, the jurisdictional review expectations. I have been burned on both of these items in the past and subsequently lost my tail on what should have been marquee jobs. Something that is always overlooked by small firms when trying to move into more significant projects or clients: The client is always going to try to control the contract to limit or eliminate risk on their part. If a client came to you with a silly deck job you would insist on controlling the fee to account for schedule, quality of the drawings you are provided to design from, review jurisdiction, and contractor, after all, you are perfectly capable of estimating the work involved in a small project like this, you know where you could lose time and increase your exposure to liability and the last thing you want to do is lose your tail on a little deck job, right? You need to carry the same attitude into the larger projects, believe me, the more sophisticated clients are aware of these risks and they are going to insist that you carry the risk, not them.
I am in the US, so these "ball park" estimates are for my market:
Based on your description:
1. You should be in a fee range of 1% to 1.5% of construction cost.
2. This sounds like a complex job with significant interaction between structure types and an existing building. I suspect that you should be budgeting something like 300-400 hours in design. Maybe more.
3. A complex building in a difficult seismic zone can bring complex analysis demands. You may have the expertise to take on these challenges, but, can you do so efficiently or is it going to eat up all your budget.
4. You can expect to put together a drawing set somewhere in the neighborhood of 20-30 sheets.
5. Your clients are likely going to be working in Revit, are you prepared to do so? Efficiently?
6. Plan review can be significant on complex school jobs, If you are in California you could be spending another 100+ hours getting this through plan review and this will come at you with little control of the schedule and with the demand that you drop EVERYTHING to commit to getting through plan review. (Note, this is something you have NO control over and which will become substantially worse if your client insists on submitting the job in a rush (which means less complete)).
7. The commitment through construction can be dependent on a number of things that are also out of your control, most importantly, the quality of the contractor and building inspector. The last school job that I did in California was a 30,000 sf gym / dining commons / wrestling room, simpler than the project that you proposed. The job generated 600+ RFI's about half of which required submittal, review, and approval by the jurisdiction. We easily spent as much time in construction support as we did in design.
Based on your description of the project and your stated experience, I would steer clear of this one. However, if you choose to take it on, I hope that this little diatribe helps you do so with a better understanding of what is in front of you.