I am using a Vitz 2004 Lavender edition FL. Previously I was using a Cultus. I can safly say that the difference between a Cultus and a Vitz is just like a difference between "Guddhaa Gari" and a proper car.
Now I give U a formula of buying a Second hand car. No matter wot tha Oddometer shows, take it for granted that the car has done 25000 km to 30000 km a year, this is a universal formula(though the exceptions are always there). All the meters are tampered in these second hand JDMs. Like when I bought my car last year it was in imaculate condition and showed only 27000 KM on the oddo but I think that as it was a 2004 and I was buying it in 2008 that meant 25000 KM multiplied by the number of years which in my case came down to 100,000 Kms.
A 100,000 Kms on an averragly maintained toyota Z Gen and in your case K Gen engines is nothing. Your engine I am sure has got a good 300,000 Km life left in it if you miantain it properly and dont run it on CNG. CNG cuts the engine life by 75%.
Now the compressor Issue. I am sure the A/C Compressor must have been faulty from Japan and ur dealer or previous owner of the car must have known it, but my dear we live in a funny country where lying & Dhokka Baazee is part of every day life. So as you have changed it now it shudint be a problem.
Now the price issue. U paid 900,000 for a car which these days is for 925,000 to 950,000 unregisterd out of the showroom. I think your should not have been anything more then 850,000 but then you saved 25,000 rupees which you wud have paid for registration, so dont think much about that at all.
Your car might have a few more glitches or nasty surprises but once wid a bit of attention and money, U will be able to manage them. Once running smooth, toyotas are prety much Bullet proof, and unarguably Toyota Vitz is the best 1000cc car in the country & arguably one of the best in the world.
Enjoy it and take care.
P.S. please for god sake do not convert it on CNG the cost difference per kilometer is not more than 2 Rupees but trust me U will ruin your car.