slow start

I bought my FJ with 3 silver-dollar sized holes in the block from thrown rods. I purchased and put in a Jasper Rebuilt (3yr/100k warranty) motor myself and have almost no issues with it (after bypassing transfer case position sensors and fixing my ADD motor). The one issue I have has me stumped...

I purchased my '07 FJ early this summer; it had thrown a rod and had two half-dollar sized holes in the block. Spent a few days, put a new motor in and it's driving fine (rebuilt in Texas with family, drove it with a trailer back up to Wyoming where I live). Recently its begun starting slow...