I cant say for sure but I know I never had any problems with my 96 bottom end to 04 headswap. No PTV even with a VT Stage 2 N/A cam with longer duration and taller lift.
with the 11cc dish that the 98 pistons have and the 42cc combustion chamber will give a ratio of 10.52. as for the milling i'm not sure. i want to get my P.I. heads milled to get a 11-11.5 compression but i'm not sure if VT Stage 2's won't cause PTV issues.