Building new stroke and bore combinations is a very specific science that that determine reliability and the personality of the engines performance. Many of the desktop engine dynos will alert you of potential problems with the pure mathmatics of a combination but they will not alert you of the mechanical problems you may run into.
The mathmatics side of bore & stroke combos are issues like improper rod to crank depature angles or thrust ratios that just will not live very long. These ratios modify the side load - dwell - and thrust angle while defining the HP / torque curves. The mechanical problems like a piston skirt hitting the camshaft or rod cap clearance to pan rail is only available in much more expensive software. This is still much cheaper than ordering custom parts to find they simply do not fit in the case with the clearances needed not to mention if they should work together in this combination or not.
Stay with packages or shelf stocked combinations so you know if the block can be messaged enough to keep you out of the water passages and if small enough base circle cams are even available. Let somebody (like the aftermarket manufacturers) with tons of dyno time and money complete the R & D to prove the benifits of a bunch of parts bolted together or if they will all bolt together.
I have a 540 inch Shafiroff comp elim. engine just sitting in the shop waiting for me to build something to put it in I will probably never get too. I had her in a 2200 pound Cobra but just got tired of having to trailer to all the car shows. I could not carry enough fuel to get there much less get home on the 17 gallon cell capacity I have. It is 12.4 C/R so needs 110 octane min. to run on gas. Alky cut my usable milage in half so a trailer queen. These guys own the market for turn-key combiations or rotating assemblies IMHO but are always trying new things in the dyno room but it is hard to beat the tried and true numbers now being delivered.