Stock Honda pistons are not compatable with eagle rods without modifications. Stock Honda pistons are slip fit with respect to the wrist pin. The wrist pin is held in place because stock Honda rods are press fit to the pin. Eagle rods are also slip fit so the wrist pin will just slide through the piston and into the cylinder wall. After market pistons have retaining rings so this won't happen. In order to run an eagle rod with a stock honda piston the piston has to have the retainer rings machined into it and the wrist pin will also need to be machined to be shorter. So basically it will cost more to machine a honda piston than to just go ahead buy a good wisco piston set.

It is not necessary to run aftermarket rods though. A stock ls rod that has arp rod bolts is plenty strong. Shotpeening wouldn't hurt if the revs are to be above 9k rpm.

12.5:1 is fine on the stock sleeves. CTR pistons will yield about 12.3:1 on an unmilled head. The compression height on the CTR pistons is .030" more than b16a/itr/Ls/gsr pistons which is about the same as the piston to deck height on a normal ls block. So these pistons basically zero deck on the block so you can't mill the block at all or the pistons will be out of the hole. Milling the head is also a bad idea. If you do run the ctr pistons I would clay check the assembly for piece of mind.

A good alternative would be some jdm b16a pistons which can get you around 11.7:1 compression or so and have the same compression height as a ls piston.