Lookin2turbo

Hello all,
Long time since I posted anything around here, but I've been doing a lot of reading. That said, I haven't found any answers to a couple of questions that I have.
So I have a 90 that I am (very slowly) working towards turbo-ing. Step one was to learn all about this megasquirt gizmo, build one and get the 1.6 running on it.
Currently I have a mostly stock 1.6 (AEM WB and variable TPS) running on the MS3 (v3.0 with MS3x expander).
It seems to be going fine but as I have been re-reading the manual getting ready to put an 02 VVT in (and subsequently a turbo) I am seeing that Section 3.5.4.4 shows that a 1N4001 flyback diode is needed for idle, VVT and boost. I thought this was all taken care of by the flyback jumper shown in 13.7. Do I need both the flyback jumper and the diode?
As I was trying to find an answer to that question I saw several of brain's posts about the 5v pullup via 1k resistor between R13 and R45. I did not put this pullup in for my 1.6 CAS (I was following the DIYautotune instructions for 90-97 CAS. Obviously I need the pullup for the VVT, but if I install it before I do the swap will it hurt my current setup?
Thanks for your help in advance.

Cutthroat912

From my understanding, the diode and the jumper achieve the same result however the diode is a more robust solution for the coil discharge. I'm currently running just a jumper simply because it is all I had at the time, and it works just fine.

I can't speak on the pullup resistor as I didn't completely build my MS3X and its been a while since I cracked it open so I don't remember if there is one in place. I also do not recall adding one when I put the VVT engine in. For my install, I followed mostly the VVT megathread for changes to the car and Trubokitty for any necessary ECU hardware changes.

Lookin2turbo

Thanks for responding. I appreciate your help. Anybody else have more definitive answers/thoughts?