There are shims available to correct your issue. Simply shim whichever side needs to be raised.
Its not a problem in the short term. The trans mount is also back 1/4 of an inch. I am actually going to shim it at the trans mount, and oval out the holes in the cross member to be able to bring it in line. For me this is the best solution. The power steering cap is slightly canted to the passenger side. So it may be some variances in the mounts causing this. But in my situation it actually will work out since it helps the pan clear the IFS.
I also had a crack in the weld on the front of the pan, so I fixed that today. I also got it fired up for a short time. Still need to wire the Alt, extend the rear 02 sensor harness, and button up and wrap some wires. Then I need to fabricate the exhaust. I have to say this thing feels like it has a ton more torque than the 22re, just when it fires up you can feel it!
Got the clutch bleed, and working fine, I am extremely happy with the feel of the clutch, very soft pedal. It also works out that it has a new Aisin clutch master and slave. I have put a lot of aftermarket clutches in, but never again, it is Aisin all the way now. Also discovered the intake I built would not work, I had to cut it to a strait tube to clear the upper radiator hose. I also ordered some T-bolt style clamps for the radiator hoses, all I can say is these things are bad to the bone, I highly recommend them on any vehicle. They are a bit pricy, but well worth it, they are about 6 bucks a clamp from summit racing.
I am excited to get this on the road, but now that I know the engine runs good, I am going to take my time and make sure it is right. This thread is great and want to thank everyone on it, this is a valuable source of info.
