There are a couple of problems with trying to go straight to J5 on the MTR2000.
The first, and biggest, is that the MTR2000 only has one active Aux Audio In path at a time, while the Zetron Model 38 puts out audio and PL / DPL on seperate lines.
On many radios / repeaters there are seperate microphone audio and flat audio inputs, that can be used simultaneously but, to the best of my knowledge, such is not the case on the MTR2000. I believe that this same limitation will also prevent you from just hanging the controller off of the MRTI port.
Additionally, I believe that there is some sort of issue with the COR signal as well.
The Zetron interface is a cable with a model 38 header on one end, and a 96 pin connector, to mate with the J5 system connector, mounted to a small circuit board with various "guts", on the other. The unit comes with outstanding, and detailed, installation and configuration instructions. An important note: the board will only work on newer MTR2000s with the J5 system coonector "right side up" (Pin A1 on the bottom left, looking at the rear of the repeater). It will not work on the older units with row A at the top.
Their tech support folks are very helpful (although I thought heads were going to explode when I told them that I had replaced their stock cable)

(I had to customize the interface to work with a second link radio as well)
Zetron considers the interface a proprietary joint design with Motorola, and will not share schematics, etc. From looking at the board, there looks to be a good number of level matching components, and an op-amp based active combiner for the audio lines. There were also pads and jumpers for some optional components in the audio paths, but none were installed or labeled on my board. I think there may have also been a transistor or two for the COR line, but I'm afraid that I don't recall off of the top of my head.
So, the short version: Interfacing with the Zetron interface board / cable is very easy. Interfacing without it is really ugly.
I'm afraid that I would have to suggest just getting the board.
Good luck!