Although it would be a cool project; but after all the cost, time/effort, etc, I think you'll have an engine that you won't be happy with. For the fraction of the cost, you could swap in a 4.0L/5.0L with a greater aftermarket with plently of room to grow. After all of that, you would have an engine (2.9L) that's meets it's mechanical limits. And how long it would actually last would be questionable. I think the only way to get this engine going good within a somewhat decent budget would be forced induction.
From the looks of the links above, stroking a 2.9L to 4.0L doesn't look feasible. Very cool links, btw!
I was there a while ago, I am actually letting go my plans for a S/C swap, once I found out forged pistons alone would cost $650 for 6. I think I'll get a full roller 5.0L that came with forged pistons from the factory. The S/C kit is going on E-bay soon (hint hint) for cheap (which I was told stock pistons are fine for it's 4-6PSI output, but I was going to get a smaller pulley for it - Eaton blower from 2000ish Nissan Xterra). Also was going to get an aftermarket PCM, etc, the whole 9 yards. If it doesn't sell, hopefully someone with an Xterra needs an extra blower.. Lots more parts, I also have a 10,000 RPM aluminum flywheel for a W/C T-5 conversion for 2.9L/4.0L (probably more for the 4.0L people). I am guessing that it works with the W/C T-4 bellhousing from a 2.8L in a early/mid 80s Mustang. Bucket seats are required.
Pete