knowledge - you pick the CPU u want and find a motherboard with the right socket, usually everything on the market is up to date on clock speeds, etc. make sure u get the right memory and install in the right order (sometimes not linear), that has burnt me on non-sequential installation of memory. Case form factor at this point afaik is atx or something extended, but that is straightforward, or just go without a case and put it in a pizza box.
time - i can understand this one well - i build my own machines for my office (4 in 2 offices, 2 each) but when they are done i avoid touching them for as long as possible. last set of 4 lasted at least 3 years, this set is over 2 years old now....the new tactic is to build 4 at the same time using identical parts in all, then install one OS on one drive and dupe the drive onto 7 identical drives (4 backups). presto-magic.
$$$$ - custom systems unfortunately aren't cheaper. the hardware flexibility may or may not be worth it to you.