I usually go through several steps with this problem, stopping when can't figure out how to go further.
First, do what you have done. Go hard with DRY. If you do not end up with a big hairy mess, you're done. If, as in your case, you have no duplicate code but each boolean has its value checked in 20 different places, go to the next step.
Second, split the code into blocks. The booleans are each referenced only once (well, maybe twice sometimes) to direct execution to the right block. With two booleans, you end up with four blocks. Each block is almost identical. DRY is gone. Do not make each block a separate method. That would be more elegant, but putting all the code in one method makes it easier, or even possible, for anyone doing maintenance to see that they have to make each change in four places. With well organized code and a tall monitor, the differences and mistakes will be almost obvious. You now have maintainable code and it will run faster than the original tangled mess.
Third, try to grab duplicate lines of code from each of your blocks and make them into nice, simple methods. Sometimes you can't do anything. Sometimes you can't do much. But every little bit you do moves you back towards DRY and makes the code just a bit easier to follow and safer to maintain. Ideally, your original method might end up with no duplicate code. At that point, you may want to split it into several methods without the boolean parameters or you may not. The convenience of the calling code is now the main concern.
I added my answer to the large number already here because of the second step. I hate duplicate code, but if it's the only intelligable way to solve a problem, do it in such a way that anyone will know at a glance what you are doing. Use multiple blocks and only one method. Make the blocks as identical as possible in names, spacing, alignments, ...everything. The differences should then jump out at the reader. It might make it obvious how to rewrite it in a DRY manner, and if not, maintaining it will be reasonably straightforward.