Blowfish has a large key setup penalty, except is fast once it gets rolling. I believe that before AES optimizations became commonplace, it was faster than AES after the initial key setup. It's top speed once it gets rolling is good for bulk encryption, except it has a 64 bit block size. Would the following address the block size limitation in terms of bulk encryption?
You encrypt the first 64 bit block with all three keys.
You then take the first key and grab the next block starting at bit 33 to 97. After that you encrypt blocks 98-162, 163-227, etc., progressing 64 bits at a time after the initial half-step.
You then transpose the bytes of the intermediate ciphertext 128 bits at a time across the entire hard drive, specifically mixing across the two 64-bit blocks. You could use a static byte level transposition, odd byes in one block and even bytes in the other. I'm looking into other ideas, such as a matrix, except for now I'm still at a static or possible key-based columnar transposition for now.
You then take the second key and grab the next block starting at bit 17 to 81. After that you encrypt blocks 82-146, 147-211, etc.
You then transpose the bytes of the intermediate ciphertext 128 bits at a time, specifically mixing across the 2 64-bit blocks.
You then take the third key and grab the next block starting at bit 9 to 73. After that you encrypt blocks 74-138, 139-203, etc., progress 64 bits at a time.
Does the key staggering complicate the MITM attack? I'm trying for triple 256 Blowfish with defense against the 64 bit block size and possibly even defense against the MITM attack.