It's hard to diagnose through chat, but since your subframe is completely refreshed, I would instead look at the block. Could be the dampener failing at a slow drip or a slight misfire from the coil pack. If you've already replaced the stock rubber balancer with a liquid one, disregard the former. Check the connection points (especially 3 & 4) on the coil pack and remove any oxidation there, be sure to reconnect with some dielectric grease for the latter. Because of the airflow through the scoop, those 3 & 4 connections tend to rust under the wire boots and cause arcing. Other than that, it's really hard to say without experiencing the problem first hand, let us know when you find it.

 

Thanks again Whiskey -
New SPI fluid crank pulley - 5K ago
Serviced / upgraded powerflex belt tensioner + belt - 3.5 k
New spark plugs/cleaned+dialectic coil - 3k ago
New K&N cone filter - 2.8k ago
The engine vibration may have been due to the altitude - thinner air as a byproduct since I've relocated from sea level to 5k above. I've done nothing to adress the cause but now, 2wo weeks later, the vibration/ rough idle has subsided quite a bit and is now idling smooth again.
New tires and a possible alignment - next
Thanks again for the continued input.

 

Update:
I have purchased and mounted 2wo new Continental Extreme Contact DWS plus 205, 45 R17s; The newly mounted tires were Hunter Road Force balanced (as recommended by NC TRACKRAT ). I could only afford 2wo tires right now. Mounted the 2wo new tires on the front and moved the less worn front tires to the rear.
It was further brought to my attention by@deepgrey that due to the increase in the weight I've subjected my Mini to recently, has caused more negative camber on the rear wheels. As a result - has worn the inside tread and ultimately altered the rear toe. I am now certain is the cause of all the vibration felt while driving. Until, I can have the Mini four wheel aligned again; I've dialed up the B14 coilovers to maximum stock height as a temporary means of helping reduce the negative rear camber. This seems to have helped a lot to get the rear wheels perpendicular to the road again.
Although, I'm really missing the tight, stiff, low and grounded feel I had before. Feels like I'm riding on a cloud with the struts now at near factory ride height.

 

Just to let you know even the JCW Race Team (LAP Motorsports) runs their race cars very near the stock ride height... Camber changes depending on the track they are at, if I remember we ran -3.5 degree front and -1.0 degree rear at Indy and 1mm toe in on the rear and I want to say 3mm toe in front. NOTE: the difference between the measurements in degree and millimeters, it is because how we measure the angles. No adjustments to ride height were made that I remember so very close to stock.

The race cars are stripped for weight but add in the massive cage and other safety items and it gets back close to stock weight.

 

Interesting. I had no idea. Although another forum member had also mentioned the cons pertaining to lowered cars on the track to have negative/adverse effects on handling.
I have lower rear adjustable controll arms on my Mini. In addition to raising the coilovers back to stock ride height, I was going to go one step further by adjusting the rear control arms to straighten out/reduce the negative camber - Although it was pointed out that it would most likely throw off the toe and possibly make handling worse without a proper alignment.

 

Here is a great link that can give you a hand at using the String Method of Alignment that you can do at home.

At Home Alignment - How To String Align Your Car | FCP Euro

 

Yep - Already done it with great success!