that's some bobo *** work there.
1- check the motor mounts are correct. might have something wacky going on there lifting the motor an additional 1/2" that you could use up front.
2- check the radiator, you might be able to space it up a 1/2" or so.
3- throw out that t-stat housing and get something decent. i don't know wtf that abortion looking thing is or what purpose it serves.
4- the manifold should have a provision for the temp sensor. install it there.
5- accordion hoses look ***. get a molded hose, or parts of a molded hose with a solid pipe slipped in there to make the connection.
6- you're likely going to need a shroud, think about that going forward.
dana hit it square with the note that the stock inlet is generally offset by several inches, which is compounding your problem here.
the easiest solution is a correct radiator and shroud, but it is also the most expensive.
