where ever it's hitting and not letting it sit properly...

I got this from Rob & Dave’s Aircooled VW Pages.

http://www.vw-resource.com/longblock.html#shroud

I hope it helps.

Doghouse Fan Shroud -
Thoroughly clean the fan and the fan housing, inside and out. Again,
painting will make the fan shroud look very nice.

Note:You can use any color you like on those engine parts that are NOT
in contact with the hot oil, but for those parts in contact with the
engine oil, black is the best color for shedding heat.

Install the alternator fan assembly into the fan housing. Make sure
the four bolts that hold the outer fan cover to the housing are
securely tightened.
Install the doghouse cover and the oil cooler vent (the vent will go
through the firewall tin.

Before attaching the thermostat connecting rod to the cooling vanes,
slip it down between cylinders #1 and #2 and make sure it will move up
and down without binding.

On the rear of the engine, reattach the thermostat connecting rod to
the right-side cooling vanes.

Carefully place the doghouse fan shroud down on top of the cylinder
cover tin, making sure that -
The thermostat connecting rod slides properly between cylinders #1 and
#2 without binding;

The oil cooler is not damaged during installation of the fan shroud.

Note: There are two engine tin screws on either side of the fan
shroud, down at the base, that hold the shroud in place. You may need
a flat-head screwdriver to pry open the cylinder tin slightly to
accommodate the shroud. (The shroud tin goes INSIDE of the cylinder
tin, all the way around.)

(My note Jim347a.  You might want to replace these two screws with two
small bolts with a 10 MM head. It makes them easier to loosen while
the engine is in the car.)

If you have removed the generator/alternator, place the two cover
plates back on and bolt them down with 10mm bolts (into captive nuts
on the other side). Use Loctite and lock washers, as these bolts
aren't something you want to lose inside the fan shroud.

Note: The fan shroud should fit tightly over the cylinder cover tin.
Screw it down on both ends of the shroud.

Slip the alternator strap around the alternator and alternator
pedestal tighten the 13mm nut.

Spin the fan and check for rubbing. You may need to level the fan and
alternator by adding a shim between the alternator pedestal and the
alternator or loosening the hold-down strap a bit. The result will be
a smooth spinning fan that can't rub on the shroud.

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I wouldn't file on the crankcase. Are you using a factory VW fanshroud
or an aftermarket unit? The factory ones I've encountered have always
dropped right into position without a fight(go figure, huh?). The
aftermarket tinware...all of it in my opinion...fits like crap. On a
good day. I've wasted plenty of time doing working on aftermarket
garbage tinware to make the screw holes line up, much less fill all
the gaps between the block and the engine compartment seal.

Chris