'93 Civic VX Smog woes..

[zug]

Two years ago, I bought a '93 Civic VX. It has been a great little car. Until I had to get it smogged.

The car passed emissions (barely), but smog tech found a second cat on the underbody of the car and failed it for a modified exhaust system.

I went to install a new cat only to find that the normal bolt on doesn't fit in the exhaust manifold and my only option was to buy a $700. The shop tech offered to swap the exhaust manifold but he was told by the supplier that doing that would also violate the modified exhaust rules. So I had the second cat removed and did a pretest, now it fails on all counts. Worse yet, the pre-tester says I have a non-standard JDM engine and I have to make an appointment with the referee.

I made sure before I bought the car that the engine had VTEC-E stamped on the top of it, and I assumed (apparently incorrectly) that that meant it had the correct VX engine.

Now I read on the forums that it's common to hollow out the engine cat and put on the underbody cat, so I really might not have a functioning cat at all.

A couple of questions:
1. How can I confirm whether or not my engine is the right engine? I know they have model numbers, but where are they stamped?
2. What the heck can I do to get this car to pass smog?

[zug]

Smog numbers, in case it's relevant:

5/21/2013 (both cats):

15mph:
RPM: 2575
%CO2: 14.4
%O2: .6
HC: Max 68 Meas 67
CO Max .59 Meas .39
NO Max 731 Meas 243

25mph
RPM: 2304
%CO2: 14.8
%O2: .3
HC: Max 44 Meas 35
CO Max.41 Meas .03
NO Max 798 Meas 569

7/24/2013 (with underbody cat removed):
15mph:
RPM: 2607
%CO2: 13.8
%O2: .8
HC: Max 68 Meas 67
CO Max .59 Meas .87
NO Max 731 Meas 659

25mph
RPM: 2298
%CO2: 13.8
%O2: .8
HC: Max 44 Meas 78
CO Max.41 Meas 1.00
NO Max 798 Meas 862