Anything mechanical said:
My nicad battery back is comprised of qty 14, 6 volt, 4ahr batteries in series. It starts at about 93 volts and goes down by tenths if a volt like a timer, losing a tenth of a volt per second.
How many amps are being drawn during the voltage drop? It should literally be a few mA. If it's in the >1A range, there is a problem in the controller.
If the battery performed fine before the controller mod, then something is wrong in the controller.
If the battery performed the same before the controller mod, then something is wrong in the battery.
If the battery was not tested on the controller before the mod, then they probably both have problems, but the drain issue would probably be a bad battery, and the controller issue is separate.
Take a household 100w incandescent (not LED, not CFL, etc) lightbulb, in a lamp with cord, and wire that cord so one end goes to the positive of the battery pack, and one end to the red wire of your multimeter. Other end of the red wire goes to the 10A plug on the meter. Switch the meter to A, highest range. Black wire of the meter goes from common/ground on meter to negative of the battery pack.
Does the lamp light up at all? Does it rapidly dim to nothing?
What current draw does the meter show?
If you have a second multimeter, have it wired across the positive and negative of the battery pack, and note down it's voltage at teh same time as the above.
You can also measure individual batteries in the string, and see if any of them are unequal voltages. They should all be very close to the same, the whole time. Any taht are significantly lower are not performing correctly.
As a side note, a 4Ah battery pack at around 80v-ish is only about 120Wh. If you're actually using it at faster speeds, it will drain to empty in only a few minutes at most, and perform badly for the last couple or more. My guess is you'd only get a couple of miles at most out of it, at 30-35mph. (it takes a lot of power to go faster, so a lot of capacity to go farther while going faster...and the more power you draw from a pack, the harder it is on it, and generally the smaller the capacity of the pack the lower it's ability to deliver high power).
It was modded to take 89 volts and hit 35 mph.
I'll have to ask this question again, since it hasnt' been answered, and the answer could be very important to solving the problem(s):
Exactly what was done to "mod" the controller?
Meaning, what specific and exact steps did you take to do the modification?
Make a list of your actual steps, lIke this list: (rather absurd, but taking some steps from actual user reports over the years) List doesn't have to be this detailed, but more detail means more chance of us figuring out which step caused the problem(s).
1-cut off all the wires
2-grind the screws off one end
3-remove that end cover
3-yank the rest of the controller board out without unbolting the heatsink bar
4-unscrew the heatsink bar from the case
5-resolder the ripped-off FETs to the controller board
6-remove the 150ohm resistors on the LVPS
7-replace them with 100ohm resistors
8-replace 63v 470uF capacitors with 100v 1000uF capacitors
9-plug controller into wall socket
10-use fire extinguisher on controller and room

11-reinstall board in case
12-reinstall screws in heatsink bar and cover
The voltage went down to about 81 volts when I turned the controller off. My volt meter showed the voltage climbing back up. I turned the controller back on and the voltage started draining again. The throttle does nothing to the motor.
Have to diagnose the drain issue first, but fixing that might fix the non-response issue. (as a side note, some controllers have an HVC as well as LVC, and wont' operate above the voltage they were designed for.)
The controller does not seem to get hot to the touch.
Then almost certainly the controller is NOT draining the battery, and the battery is simply not any good (doesn't actually hold any significant capacity, needs to be replaced).
In order to drain as fast as you're reporting, it would probably need to be pulling many amps. At dozens of volts, even a smaller drain like 10A would mean hundreds of watts, and the controller would heat up like a hair dryer. (quite possibly it would actually smoke, depending on the specific failure inside)