Sync issue recording drums using both midi and audio inputs

I'm not quite sure what you are asking here.

Do you mean there is a 4ms gap between you hitting a pad and the audio emerging from Sonar? If so, that's pretty good and will require a lot of work to get any smaller - if it can be done at all. 4ms is like listening to something from 4 feet away.

If you mean that there is a 4ms discrepancy in Sonar between the MIDI track and the recorded audio there are several ways to correct that. One is to select the audio and drag it to where you want it or select it and use the nudge command.

Another is to tweak the MIDI compensation buffer in preferences. Though this has the disadvantage that if corrected for one synth may make sync issues worse with others. The MIDI clock might not be regular and accurate enough to give timings that are spot on accurate either. Most DAWs don't clock perfectly and neither does most MIDI hardware.

Any MIDI device, be it a VSTi, a hardware sinth, a USB inteface, whatever, requires some time to do its job. This can lead to slight audio/MIDI sync discrepancies. To be honest, if it wasn't for being able to see the discrepancy on the screen when zoomed in I doubt anyone would notice a 4ms difference. A drummer listening to their band through stage monitors is going to be hearing the band at least that "late" and no-one seems to notice that.

In theory yes Sonar does have tools to automatically align MIDI and audio, usually when the MIDI is generating audio from an external hardware synth. There's a serting in advanced preferences that can be tweaked if necessary, but in the real world correcting a sync discrepancy for one MIDI interface or synth doesn't help much if you use several.

Other than that, you can quantise audio and MIDI, extract groove timings from either and all kinds of things. The manual/help can take you through doing that probably better than I can.

I assume you monitor by hearing the acoustic drums and the MIDI is used later to trigger a sampler/synth in Sonar? If that's the case and the problem is Sonar is placing the MIDI a little late then one option is to select all the MIDI and quantise it to a very small time interval. Whatever you do you may find you need to do some manual editing to get the drum samples lined up to make the recorded drums sound OK. Spot on timing may or may not be the answer, because your timing may not be millisecond accurate (I know mine isn't) and a dead accurate MIDI track won't help if it's still not in sync with the audio.

One option might be to re-record the cymbals while listening to the edited/quantised and now correctly timed MIDI/sampler drum track.