I haven't replaced our front struts - one reason being similar reports to yours I have read here, with indications that this is normal.

The dust boots not fitting seems suspicious, though, I would quadruple check for correct part on the replacement. Also, you did not indicate that any alignment was done. A raised suspension will change camber, caster, AND toe, so this could account for the handling issues. Also, if the new ride height is removing too much vertical dynamic range, this would cause handling problems when going over bumps.

Finally, raising the rear will shift the cg toward the front, and will likely lower the front ride height a bit. It will also shift the suspension geometry back toward its previous condition. However, when I replaced our rear shocks, any change in ride height was not obvious. It turned out the old shocks were not as badly worn as I had thought (were not the cause of the handling issue of the moment).

Steve