The upgrade process for the Sony PC you want to modernize isn't exactly going to be easy, nor is it possible with the current stock parts. I've never worked with one, but it looks like an mATX standardized (Minus maybe a few specifics) motherboard, but if you look at, say, the [guide|1235|Teardown] of said computer the computer ends up using some proprietary ports for the front panel, which can be problematic.
The system you want to build is 64-Bit. This computer only lets you use one of 4 series of 32-Bit processors. In short, you cannot upgrade this computer. You might be able to buy a new set of parts to leave behind the IDE years, but there isn't any true "Upgrading" with the parts you currently have inside that PC. On top of that, fabricating is likely inevitable to replace or interchange certain ports.
I say keep that PC for certain workloads (specific XP-related stuff, for example) and build a new one. A decent low-end PC can cost maybe around $200 or maybe more currently. Just my opinion.