I am looking to see if anyone has found a plug and play replacement tuck/milspec type harness for the obd2 cars, specifically the 99-00 civic.
Alternatively has anyone removed the looming material and replaced it with a nicer looking heatshrink?
Thanks.

 

Not sure about the plug and play, I do not think so, but replacing the convoluted tubing with shrink tubing would be a very big job and would require de-pining a number of plugs as the shrink tube would not go over the plug.
A lot easier is to back tape the harness, also fair amount of work, but is a lot cleaner and makes for a smaller diameter wire bundle, this is best done during a tuck when harness are out and you can lay them out on a table.
To start you would remove the convoluted tubing and any tape, make your extensions, [solder and shrink tube them] get rid of as many overlapping/twisted leads in the bundle, [parallel the leads] then start taping, using good quality electrical tape, with the first layer of tape wrapped around wire bundle "backwards/upside down" [sticky side outside] with about 1/3-1/2 with overlap, then back tape over that with stick side down, [sticky sides towards each other] this makes the sticky sides of tape stick to each other and not to the wire bundle itself, this makes the bundle very flexible and allows for very tight turns, paralleling the leads, [not allowing leads to crisscross each other in the bundle] makes for a smaller diameter bundle, again a fair amount of work, but once done looks and functions well.

I have done this many times, most of the time using black electrical tape, but have also used black friction tape, [hockey tape] for an old school look and colored tape, [mostly to match engine bay colors], sad to say even some but ugly stuff like the florescent orange tape on a tuck for a guy with a Ford Focus that was riced out, the 79 Ford F250 I am rewiring now, [Painless harness] will be old school friction tape to kind of match the original cloth sleeves use on some of the stock wiring. 94