If you just connected the original wiring to a new coil the resistor will still be active and the new coil won't like it.
Start the engine - sounds like it will idle OK in Park - put a multimeter on it, positive lead to coil positive, negative lead to a good earth. If it reads 12 volts or more your issue isn't the resistor still being in the circuit. If it reads 9 or so, the resistor is still active.
The pink resistor wire is found at the back of the starter switch. You may have to google how to remove the switch. A few centimetres downstream of the switch there is a kind of bulge in the pink wire which is the resistor. On the engine side of the firewall this pink wire changes colour.
As Shane said, you can either connect a new wire direct to the starter switch, or use the pink wire - whatever colour it is under the bonnet - to trigger a relay that then connects 12 volts direct from the battery.
All of that said, reading the symptoms again I'm starting to think this won't be the issue (but its easy to check and fix so worth doing). As I said, mine wouldn't idle below about 1,200 revs until I sorted this out. It sounds like your's is OK at normal idle in Park but can't handle the 100 or so rpm drop when it goes into gear.
I wonder if its some sort of weird issue with the neutral safety switch?
Anyway, I'm sure you'll get it sorted.