I currently have a 95 tracker pro 18 jet minus the inboard motor. it is getting an alluminum plate welded to the transom so we can mount a 50 horse merc so thats around 5 thousand  for a motor. however  i found a 1992 skeeter 200 cdx with a 03 mercury 200 that appears to be in great condition and the person wants 8995 for it which option should i go for a new motor on my tracker or the skeeter?

Value wise, that tracker won't be worth beans after you do the mods.   Making a boat built for an inboard boat into an outboard, doubt many people would care for it once you decide that's not what you want.

besides the low to nonexistent resale value on the tracker how would it perform with a 50 horse mercury 2 stroke as far as top speed and such

So you want to modify a boat to put a 50 on it when you can buy the glass boat with a 200 ready to go? You should be out closing the deal on the Skeeter instead of typing the question on this website.

Go get it and enjoy.

i say the skeeter is in near perfect condition, however what are some things i should really look at before buying it, im still unsure about buying a 16yr old bass boat

A Skeeter of that era?

The wood in the transom, stringers and floors are immediately suspect.