Hey crazy, I just went through a set of '93 250 forks, (seals wiper & fluid change) one fork seemed to be wasted and was only a $22.oo inner fork rod broken. seals, oil, wiper and inner rod was only about $100.00. (yea labor was free)
You might want to dis-assemble the forks and see exactly what's up. Before you spend any more $'s.
You got the engine figured out, the suspension is really not any more complicated.. I know it's not the same as a newer suspension, however getting the present set-up re-sprung and valved for you might be the least expensive option.
Maybe some of the other guys who have had their suspension re-built and re-valved (tuned for them) will chime in.
Tuck\o/