Get one that already has the mods that yer lookin for done... provided that they're done right! Often it's cheaper in the long run to buy one that's got the SPOA, lockers, gearing and such done so that you don't have to spend the time or extra $ on it. The engine swap is another issue however... I've done my own 16v conversion and it is time intensive and can be expensive... upwards of 3K. On the other hand I've seen some conversions that are hack jobs... ya they run, but nothin to look at... really mickey moused.
I know a guy that bought one with the coils, lockers, seats, wheels & tires, & 16v conversion for right around 6k... is that a fair price? well, I think that's about what it'll cost whether you do it yerself or buy it thata way... If'n you DIY you'll at least do it the way YOU want.
If you need specifics on the maladies of the Samurai's they are:
Dist gasket/o-ring leak back of head
Tranny whine (bearings going)
hard start (relay clicky start problem)
Heater not hot (core plugged externally w/leaves & such)
Overheating (bad radiator)
Electric Gremlins (poor ground)
Door handles (cheap plastic) get good ones from PetroWorks
Window rattle (bad runner gaskets) get good ones from PetroWorks
Other than these things the Sami is very sturdy and a whole lotta fun.