heres more to the steps. i find it best to use anitseeze as a marker to fine these holes. first put some masking tape (4-6 layers) on the bottom of the plate and bolt it onto the engine mount (not yet the tranny) then anti seeze on the tranny holes remember they are not touching yet. then you use a jack and jack up the tranny so it hits the mount (remeber the mount is in place just not bolted on the tranny) this will give you holes as a guideline to drill. however before you can do this step you'll already have needed to complete grinding metal off of the shift levers on the tranny (the last pic shown on the fist post i did). if not the plate will not sit right.
this is what the plate should look like after the holes are drilled.
make sure you use longer bolts (left overs from the old engine parts) and a big washer for this part. i've even gone for far as to use thread lock (blue) on it.

this is the finished product.

as far as the shifting goes your stock shift linkages work, but to clear reverse you'll need to modify the shifter base. firstly the base is of 2 parts a casted (heavy) pieace where the shifter bolts to and the bottom of that where it bolts to the car. take the top half of and grind under it at an angle. this part is trial and error because i really can't tell you how much to grind of. you'll have to keep grinding and refitting untill it clears or is right. next the mounting base is the cut one little section where the passenger side linkage sites. when you test mount the shifter you'll notice if you go left to try and get into R the passenger side cable will hit the mount plate. this is because it is now traveling a farther distance that what it was orignially designed for. the last step is to cut a hole on the passenger side for the sifter to clear such as in this picture.

just a hole be mindful to to cut it out. also everthing in these speps are exsagerated even more for a TRD short shifter. more grinding bigger hole. reason why i know is because i mod it to work for the stock shifter. then i had to mod it even more when my TRD shifter came in.