Most "kits" that you buy from say SCAT or Eagle have "stroker" rods that are already made to clear the cam, cylider wall bottoms and the pan rails. It is still a really good idea to mock the engine up and turn it over slowly to see if there are any problem areas which you can just take a die-grider to those areas of the block.
If you aren't trying to make tons of power, just say in the 430-470hp and 440-480tq range then you would do fine in buying an externally balanced rotating kit with "hyper" pistons instead of forged. I would assume that you are planning on changing the heads as well. Look for a set in the 195-200cc intake runner range: AFR, DART, Brodix are who I would recomend. If you are on a budget then the DART platinum iron heads are the greatest deal for the money IMHO. To run easily run pump gas with a pair of 64cc combustion chamber iron heads you will want to look for a piston with a 15-18cc dish. This will put the compression right in the range of 9.5-9.8:1.
IMHO your rocker ratio choice should depend on whether you going to run a flat tappet cam or a roller cam. If you plan to go cheaper with a flat tappet cam then I would suggest just going with a 1.5 rocker ratio, but if you plan to spend a bit more money (which is WELL worth it) and go with a roller cam then I would go with the 1.6 rocker ratio.
Your gear ratio really be a well thought out choice. The size of your tire, cam you plan to use, use of the vehicle, weight of the vehicle, the last gear in the transmission, and the desired cruising speed are all factors in selecting your rear gears.
The 3.73:1 gears you mentioned would work great in the TKO 600. When you calculate out the 2.87/1.89/1.28/1.00/0.64 gears of the TKO 600 with 3.73, the final drive ratio is almost identical to using a th350 with a set of 4.10:1 gears. When you calculate out the TKO 500 which has 3.27/1.98/1.34/1.00/0.68 with the 3.73 rear gears it comes out to be really close to what a th350 would be with a set of 4.56:1 gears (all done 1-3rd).
but again it all depends on what kind of use this car is going to get and what kind of cam this car is going to get. putting it all together with a set of 28" tall tires the TKO 600 and 3.73's would do great with a cam in the 220-240° @ .050 duration area, which would make for a pretty decent street car with some track use. The TKO 500 and 3.73's would do better with a cam in the 235-250° @ .050 duration area, which this motor would want a bit more compression (Iron= 10:1+ and alm 10.5:1+, which could still be tuned to run fine on pump gas) this would make for more of street/strip car with a bit less street manors. Both are still very do able for the street, you just have to decied how far you want to go with it.