I would agree with not caring about the value part of the car if the OP plans on keeping it for years to come. Rebuilds often turn out to be very good but at the same time, they often end up being horror stories, with the mechanic blaming the kharadiya, the kharadiya blaming the parts supplier, the parts supplier blaming the mechanic. And you end up getting disheartened with your car and selling it. True, the same fate can be met with swapping the engine if not done properly, but if done properly, the chances of that happening are low.
Now coming to the engine. There are two types of 1nz-fe available in the market. The earlier generation 1nz and the later generation 1nz which comes in Axio, Premio, Vitz Rs and the sort and is marked as "R1nz-fe". The R1nz is drive by wire (electronic throttle) and would require major changes in the wiring of the car as the interface used in that engine is completely different and it runs off of CAN bus. That variant of 1nzfe is mated to a CVT auto transmission and the ecu can only work with a CVT transmission and a pedal sensor would also need to be fitted. The CVT transmission alone costs in the vicinity of 75-90k and even if you buy it, you wont be able to make it work because it requires input from the ABS controller for it to work. Now, you're left with the option of installing the earlier generation 1nz-fe which should work fine with your current transmission. But since you said that the transmission has completed its life as well (if I read correctly) you may use the transmission that comes in corolla X or fielder which is the U340e I guess.
Another way of going about it is to buy the later gen R1nz-fe and convert it to non-drive by wire. I would recommend you to do this because it would be easier to find the later gen one in good condition with low miles on it. To do so, you'll require to replace the intake manifold with the older gen one along with the cable driven throttle body. The knock sensor would also need to be replaced with the earlier gen one. This should cost you around 5-7k additional but would somewhat ensure that you'll get a healthier engine. Then its just a matter of hooking up the stock wiring and replacing the ecu with the 1nz-fe one from a fielder/corolla x. Talking about ecus, there are two kinds of ecus. One that is taken out of vitz and the likes and one that is taken out of corolla / fielder. The market is flooded with the vitz one and it would set you back about 1-1.5k, while the other one would cost about 6-7k. The difference between the two would be that the vitz one doesnt send the appropriate signal for the temperature gauge to work since there is no temperature gauge in vitz, there are only lights, so your temp gauge will not work with that ecu. You'll need to get the other one for the temp gauge to work. The kabariyas / electrician would recommend you to get the 'kit' (the temp gauge) replaced inside the gauge cluster and would install a temperature sender somewhere in the coolant stream. I would recommend you not to have that done and spend a little more on the proper ecu for peace of mind and for saving your cluster from being butchered.
Hope that helps.