I am no expert by any means but I have been around the block a couple of times.
http://<promotion of site not allowed>/UJ675
I found this for about $250 on ebay.
If I was on a budget I would've personally chosen this simply over processor family (i5 vs Core2duo) and HDD superiority (320GB vs 500GB).
Other than that I would try to go for the largest screen resolution and Video capabilities.
There are a couple T60ps with 15.4" TFT display with 1680x1050 (WSXGA+) and ATI graphics with 256 MB dedicated video going for about $250.
http://www.thinkwiki.org/wiki/Buyers_Guide
The link above can be really helpful when deciding on what thinkpad to choose.
And below we have /g/s guide to thinkpads
http://<promotion of site not allowed>/UJ8IL
Make sure you take a look at both of them.
As far as your questions go.
Anything you buy second hand just make sure it isn't over heating and that the screen isn't dim or come with other imperfections such as dead pixels/scratches etc etc.
You can always build or get someone else to build your own frankenpad with the components you want and at a budget.
On the differences between x64 and x86_32 below is an excellent article on what the cons and pros are.
http://<promotion of site not allowed>/UJBUJ
I would always recommend x64 over x86 due to its memory transfer limitations you decide.
Thinkvantage Bioses are simply the proprietary Bios variant of IBM/Lenovo computers as when compared with Phoenix, Dell and Award Bioses.
As far as paying too much goes. Like I said that is a matter of how much dedicated video if any the T400 you got has, the speed of your HDD 7200 vs 5400 rpm and its resolution.
Welcome to the forum and please enjoy your stay.