hi, ive owned 2 of these bikes and they are great all round and very reliable. the clutch cant be too bad if it can 4th gear wheelie. however the plates are cheap to buy as they fit several years of the yz/wr engines and easily available. replacing them is not a big job but if in doubt of your mechanical skills then beg borrow or steal a owners manual which shows you how to do the job (along with any other work on the bike you may have to do!).
the gearbox issue is not really a common weak point on the wr250 but can be common on any older 2stroke gearbox. it will be expensive to fix and i doubt its something you would be able to do yourself (big job..motor out, split cases,new gbox parts etc..). cheap option is either live with it, or use a rear sprocket with a couple more teeth to lower the final drive ratio and make starting in second gear a bit easier (dont use first anymore), ok so the bike wont have as much top speed but most people dont use full throttle in top gear all that often anyway.
p.s. lots of second hand parts on sale on b-bay.