Depends on who does the axles, but $300-400 per axle is average where I live. This could be higher where you are. Add in the cost of an alignment ($100). The flex pipe reference is pretty vague, but estimate another $200-300. Windshield could be $200-300 again.
Have you seen a receipt for the "rebuild"? A lot of times, the engine was opened up and valves and rings done for a few hundred and the seller will tell you it was a rebuild. A lot of times, the claim is pure fiction, or no more than a dose of "mechanic in a can".
You could easily have two grand in the car by the time you're done, just doing what you KNOW is bad, not to mention what you find later (you WILL find other problems, like a transaxle that is suffering from exposure to bad axles, which could easily cost another two grand).
Sounds like a money pit.
BTW, don't even think about driving the car with bad axles. In addition to possible damage to the transaxle, if one of these guys fails completely while you are driving, you will lose control of the car and probably wreck it.
Good cars in your price range are very hard to find, since used parts like transmissions and engines sell for more than this entire car.