HondaCivicForum.com - Simple swap questions (I think)

I DON'T CARE TOO MUCH ABOUT HORSE POWER

Ok, so ... I have a 1998 DX hatchback with 136k miles. I had it for about two years and 20k miles and it never gave me any problems (beside an axle, two front tires and the regular tune-up).
The last time I took it to the mechanic, he told me that there are 2 problems with it: the engine mounts and the main crank(shaft) seal. He also told me that the car is not really worth the money fixing it (he also told me that he wants to buy it from me).
Both problems are not that bad and he told me that if I watch the oil level, I can still drive it for a year or two before it gets really bad (seal mainly, the mounts might last even more). He suggested me to drive it until it (almost) breaks down and then think about either a swap or sell it to him.
There are 3 more things/problems with the car: a valve clatter (it might be nothing), 1st gear whine (which didn't get worse after two years) and the pressure plate bearing (which screeches some time - still not getting worse after two years).
As you can see, there are enough reasons to think about a (sensible) swap. I thought about it for a while and I kinda reached a conclusion but I still need some information/suggestions/reassurance.
I decided to go with either a D16Y5 or a D17A6. The car is mainly used for commuting and short trips so fuel economy and reliability is first, horse power is last.
I know that D16Y5 has the same engine block so the swap is easier. The question is: how much different is the D17A6?
Where should I get the engine from? Is http://www.car-part.com good enough as a starting point?
In both cases, do I need anything more than engine/transmission/ecu?
Is is worth going with the D17A6 compared to the D16Y5 (a bit more power/torque, newer engine, reliability)?
What an I looking at, price wise?

Please help and thank you in advance!