Answer:
As with any engine rebuild, you will have to make the decision to rebuild or buy a replacement engine. The replacement engine can be new, used or remanufactured. I do not recommend a novice rebuild their engine, unless they can afford to make a few mistakes and accept that as the price of education. With that said, any rebuild will include the following...
1. Compression check if possible before removal of engine. Check compression on all 4 cylinders paying attention to the maximum value as well as the difference between cylinders. Compression should be around 130 - 160 psi depending on how much wear there is in the cylinder. If compression values are low in any cylinders a leak-down test will need to be performed to determine where you are losing compression. Possible suspects are bent valves or worn rings.
2. Once the engine is removed and stripped down, measure the cylinder bores and pistons for wear. If within factory specs you can get away with a hone job and replacing rings. More often than not, you will have to bore the cylinders which will require new pistons and rings.
3. You seem to have a handle on the crankshaft, but I would check into a replacement crankshaft, sometimes they can be cheaper than getting your crank refinished. With the crank out, check the main bearing webs for cracks and wear. If you spun one of the bearings in it's seat, you will have to have the block align honed.
4. Depending on the mileage on the engine, you should also consider getting the cylinder head refinished. At minimum it should be checked for cracks/warpage and new valve seals installed. Any competent machine shop can check for cracks and warpage as well as change the valve seals.
5. When re-assembling the engine, here is a typical list of required new parts you should purchase. Full gasket set, oil pump, water pump, timing belt or chain, timing belt or chain tensioner, oxygen sensor, air filter, oil filter, and fresh oil.
Now that you know what is involved, take a look at your local salvage yard for a low mileage engine and compare pricing. It may be worth your time to find a 30,000 mile engine from a wreck instead of rebuilding your engine. Also as mentioned before a remanufactured engine may be price wise depending on where you are and availability.
Good Luck,
Kevin