The MBR is something you have no need, or want, to mess with. It is a small section on the hard drive that maps out some basic areas of the drive. The problem you are seeing has nothing to do with the MBR.
There are two factors involved in the slowdown of the system over time. 1) The addition of drivers and programs, and 2) the fragmentation of the data caused by 1 and by deleteing files. Basically, files are differing sizes that can be quite large. To account for the fact that it is very doubtful to fight a file on a continous area of disk, the system will fragment the files.
When you format a drive, depending on file system and size, the disk is divided into clusters. A cluster is the smallest amount of addressable space on a hard disk. They can be small (512 bytes) with good file systems (UNIX, Verilog, etc.) or large (32k) with older file systems (FAT16 on a large drive). What happens is when the data is stored on the disk, it is split up into these clusters, and placed in any available clusters. As you delete, move, add files, some clusters get freed up in certain areas, and the filled up with other files. You will start getting files that have their clusters spread all over the place. The problem (and hence your problem you see) is that hard drives are made to be very quick when reading data in a continous area, but can be a bit slower when reading data that is scattered (fragmented).
The way to help this is a defragment program (Windows has one). There can be different settings depending on how you want the data laid out, but in essence, these programs will reorganize the data on your hard drive so that the clusters of a file are continous. That way the harddrive cache will be useful, and the system will speed up.
BTW, what keeps track of the file allocation on a hard drive is the file system table. For Windows 9x, it is the FAT (16 or 32) table. Like the MBR, this is not a table you want to mess with on your own. It is a mapping table os all the clusters on your harddisk. Messing with it will only make you lose data (unless you really know what you are doing).