Thinkcentre A55 (9265-7HG) (The machine of friends of mine, bought on my advice) refurbished last summer -does not run properly - advice and help welcome,

It is a thinkcentre A55, bought new some 4 Years ago, once serviced (autom 2009winter 2010) by lenovo (sadly: I do not know what was done).
In summer 2010 the machine came back to me (I did the initial installation), its hdd was nearly completely used, no space left, the main userID was corrupted (multiple restored copies found), Kaspersky showed some systemfiles as suspicious, the machine did not run properly.
I did exchange the hhd (new: 2TB Hitachi, SATA), add 4GB of memory, exchange the CPU (D945 for a D925) and I did add a diskrete/additional graphics-card (ATI, PCI-E16x, 256-512MB). I did no new installation, but cleaned the existing one; defragemented it, added neccessary new drivers, deleted the old and no longer needed ones and last not least updated all software and drivers. When I handed it back, it run smoothly.
This winter (2011) I had it back, very slow. I did another clean up. But after some weeks it is back again to slow motion.

Any hints would be helpful:
Will I have to go for - another powersupply (as the graphics-card does consume more power), another motherboard (as for age) or another memory/cpu - or else just be forced to redo the installation, preferably Windows 7 Pro (may be I should have done so before)?


Any Help or experience or advice is welcome

P.S: Is a HDS722020ALA330 Deskstar 7K2000 2TB SATAII 7200rpm a problem, if there was a SATA-Drive before (160GB, non Hitachi) ?