It sounds like you are on the right track. People don't realize just how big a 100k furnace is. It is too big for most houses in most of the country. It sounds like the lowest cost option might be a smaller/modulating gas furnace with maybe some duct rework for the garage area (might be as simple as adding a return or might need a larger supply). You could also supplement the garage heat with something like resistance electric (cheap to install, expensive to run) or perhaps a mini-split (which would cost more to install, but less to run).
Now, if you are willing to spend more (along with the work that goes with it), there are many more options. A boiler could work, but would be costly to retrofit (although could give some nice features like the indirect WH). You might also go with a couple mini-splits in the house and ditch the furnace and ductwork altogether. Mini-splits are very efficient and will heat and cool without ductwork. As an additional plus, you could pull out the old ductwork and maybe gain a bit of space in the house(remove some bulkheads/duct chases).
I think that I would go for the mini-splits or a new gas furnace based on costs and your location. However, things the you want (like the heated floors) as well as any other renos that you were planning at the same time could put the boiler as a contender.