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The motor is in an ED hatch everything converted to obd1 if that helps any.

 

is the idle surging?

 

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Get rid of the SAFC. You don't need it, you already have a tuneable P28. Go get it tuned somewhere. And don't say "it's already tuned", because if it was, it wouldn't run like shit.
Running like that isn't anything to do with being a built motor, you don't have big lumpy cams or anything like that. It's not stock, but it's made with stock parts, there is nothing that can't be properly tuned with that ECU.
It's also possible that you have a sensor problem, or an idle air control valve (IACV) problem, but I doubt it. IACV problems are fairly easy to troubleshoot thought.

I'd get rid of the SAFC and go from there, there's no reason to have one and it's just going to complicate (and possibly interfere with) your ECU tuning.

 

idle bouncing up & down sounds like IACV or FITV. most likely is IACV very common problem with Hondas.

 

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I wouldn't be with that small amount of variance, if it still does it when it is at running temp, it may be a TPS. 1300-1400 is kind of high but I don't know how your ECU has been tuned.

 

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... exactly...