Detailing, compounding, stone chips and engine cleaning

I purchased a rotary and being a novice followed lots of guides.
As far as I was concerned the paint is original good condition and though there were some marring and tarring mainly on the front that needed detailing especially being white when cleaning car these would show up. 
Note I bought car recently these were t that apparent maybe cos of polish wax or because I left it at a Waxoyling garage and the chap Waxoyled and left it under  a cover for two months whilst paintwork was still dirty with road dirt. 
Anyway having driven her back home 20 mile trip more road dirt I like an idiot left it under a car cover fir anotger few weeks till I had time to peek under and wash her. To my horror there were nasty grease smudges and all sorts of contamination on the hood that had been aggravated from being under the cover. 
I washed dried and discovered contaminants and harsh feel on mainly bonnet and some panels. It was getting dark so out came the cover and I stored it away for the Following week as in this weekend.
I got my hands on a lightweight rotary armed with Wash wax 3M clay bar I set to task. Clayed as much contaminant to try and get a smooth finish I could tell especially on bonnet there were previous chip repairs miniscule pock  marks that had been part of the original touch up. I then set to mopping g or compounding with a light abrasive fine G3 Extra liquid. I got good results on bonnet being mindful not to burn or agitate the weaker front lip of bonnet. I completed rest of car wings doors quarters with rotary but switched to hand polishing lines ridges and smaller sections. A pillars tops of doors and bootlid and bumpers. I even washed and laundered the car cover so as not to transfer any contamination after polishing and waxing.
However I had one mishap when buffing the bottom part of  left wing the bottom of the pad spinning at a low to medium speed caught the side bumper on top part facing up. I thought nothing of it but when I looked down I saw two half centimetre width round chips and realised I must have agitated some raised paint or small flaking raised chips. I felt cursed especially after many people walking past my driveway both young and old commented on what a lovely car and how good condition and clean it was ???
 Question is whats best way of masking these, the cars Alpine white and you can see the black either primer or base coat of bumper. I also noticed tiny micro pock mark chips dotted one of the rear arches these are close together Is there a product that can fill these ? 
Lastly the engine bay is unsightly especially after the waxoyling on the inner flitches the Spray from underneath chassis mixed with the clear coat from the top. I was hoping he would have steamed the engine and the bay before applying clear Waxoyl but the donut didn't claiming he didn't want to disturb the sealant (I could understand this but at least take off the surface dirt). I also had the chap shove loads of Waxoyl inside the bonnet. 
Any advice how best I should clean engine and the bay without compromising the integrity of the Waxoyl. I have TFR/Engine degreaser, I have a steam cleaner was thinking if using it liberally/sparingly and some brushes??

I haven't found that TRF or Degreaser Shifts Waxoyl although mine had been on for 30 yrs, the only stuff that seems to shift it is White Spirit, so as long as you don't have any if this in your cleaner, you should be able to smarten up your engine bay.  Just test a small area first.

I did try steam on my engine, and worked well, but on the areas where waxoyl was, it just melted it and sprayed it elsewhere, so use the steamer where you have oil and general print, but not on waxoyl unless you want to remove it, when a combo of steam and white spirit will remove it with ease