bruce19

Caveat: I haven't read all the responses so my comments might be redundant. For $3500 you can buy a new bike that will be an improvement. One example is a CAAD 13 but there are several, if you can find one. You might also find something used at a site like The Pro's Closet. I recently bought a Guru Photon (2016) that is all Dura Ace mechanical and weighs 15 lb 3 oz as ridden. It cost me $2500. As for upgrades......in my 40 yrs of cycling the best upgrade I have ever made has been Mavic Ksyrium Elite USTs (tubeless). They are lighter, smoother, more comfortable and spin up faster.

Chuck M 

IMHO, I think the tires, clipless pedals and bike fit suggestions are quick routes to achieving the faster and comfortable goals the OP stated they are looking for. I suspect wanting to do these things in conjunction with recently getting into cycling has brought on a case of upgraditis. Throwing $3500 at this may lead to some disappointment and discouragement that knocks some of the luster off of this new hobby. A good diet, and strengthening the core will not dig into that $3500 nest egg but will also help with speed gains and comfort.

Someone already suggested riding and identifying what you like and don't like about the current bike for a while. I think that is a good strategy for the OP.