Cabinets are fairly easily replaced but the process may damage counter tops. Extreme care must be taken while removing and installing cabinets to prevent damage to the floor. Asking for trouble? You bet-cha!
At this point you are stuck with matching the same cabinets unless you reconfigure flooring and counters. Manufactured cabinets generally come in standard sizes and are easily replaced. A base cabinet 24 inches wide can be a drawer or door base, so you can make some minor changes in style and function while keeping to the same plan and sizes. Measure existing cabinets and price out the entire replacement. I assume you will keep the new wall oven enclosure.
Your existing cabinets are probably screwed to each other through the vertical stiles and to the wall. Those screws need to be removed. Countertops may be screwed, nailed and/or glued to the cabinets. It will be hard to remove the counter without damage. Your best bet is to remove all fixtures (sinks, cooktops), and cut the counters off. Done right, this will destroy the old cabinets but leave the counters intact. If the counter includes glued miters or corners you are probably sunk, count on replacement. After new cabinets are in, floors can be matched up using a strip of shoe molding.
Your instinct that it would have been better to do this before the floor and counter was correct, but even cheap cabinets will be a larger overall investment than the floor and counter you installed. The project is worth it if you can afford it and it makes you happy. Good luck.