I picked up a 96 Probe years about 5 years ago for the same reason. It was at 230K, and had not been taken care of by previous owner. A lot worse condition than yours sounds like.
I agree with LIMA and Dan, do a compression test and check for any signs of bad leaks. No point in replacing more than needed. My Probe needed a head gasket and more, but didn't discover it until after replacing the clutch (practically had engine pulled to do that).
If you are pretty confident that you want to go through the motor and you have room to do it I recommend dropping both the motor and trans and working on the outside the car. Open the engine check out the cylinder walls, if the look decent (google will tell you more than I can) then you can probably get away with honing instead of boring. I opened that Probe and still saw some cross hatching and decent cylinders, got away with a hone and standard size pistons. If cylinders look rough you'll need to have them bored, take it to a machine shop and they'll tell you what size to get. You need to do that before ordering anything.
Check on the price of having a crank checked and machined locally. Compare that to the price of a crankshaft kit for your car, it includes a reman. crankshaft and appropriately sized bushings for it. If the price is right for getting yours machined they will tell you the bushings sizes you need to order with the kit. My local prices getting the crank kit was cheaper than machining, but I didn't have that option anyway due to a thrust surface being damaged.
Get the other Master Kit, EK310M, it includes a timing kit. If you are going to the trouble to rebuild the motor you need to replace those components as well. I also recommend getting a new oil pump and water pump. You will have a practically new motor going back in, you don't want to be counting on a 250K oil or water pump. You may also need new head bolts, many engines now use torque to yield bolts (-aka- one time use).
Special tools... Repair manual (Haynes or Chiltons at least) for your car, it'll have instructions and torque values for disassembling and reassembling the motor. Torque wrenches and any special sockets and bits that are required. I imagine nearly everything on that motor will be metric so a good socket set in that and you'll probably need a couple of larger sizes than are in the set, but I can't tell you which ones. Pry bars are very handy tools, but be careful with them. You may also need some special tooling for setting the timing on the motor, the repair manual should be able to tell you more about that.
On that Probe I didn't do everything at once, that's probably the main reason I no longer have it. Basically had the engine and trans pulled 3 different times in the first 2 month of owning it. Once it was right it ran great for a year before third went out in the transmission. Didn't want to pull them again and I was having trouble with my other vehicle (recurring head gasket problem). The probe got donated to the local tech school, and I bought a new car with warranty. Still kicking myself in the azz for that one. The automatic and warranty are nice, but the manual and beater was more fun.
Welcome Visitor! Please take a few seconds and 
