Which motor to buy and build?
 

I have a 99 that threw a rod. So short story is I need to buy a replacement. I can either get a 05 msm turbo long block for 2100 or a 96 1.8 for 1400. The 05 has around 165 compression across all cylinders and 96 has 175. Question is which one should I buy?

Both no VVT. The MSM head ist the better flowing BP4W head (like your old one). Your 99 intake manifold will NOT fit the old NA engine, so I would get one out of an NB

The MSM
Better head 10-20% better flow
Better intake camshaft
MBSP
VVT oil pump
9 years newer
Better oil pan
Better engine mounts
Already set up for turbo, oil drain and oil feed on left side of block (96 might have this)
Better cam sensor.
Shims instead of HLAs
The list goes on...
And if it comes with the valve cover and original oil cap you can recoup some of your money and re-use you 99 stuff