Go with your gut first, and checkbook second. We all work extremely hard for our money and it is very understandable why saving $1000 (for example) by choosing the contractor with the lower bid is an enticing option. But nothing is worse than spending $8000 on a project and having a bad experience when you could have spent $9000 with another contractor and had a very pleasant experience.
That being said, if you received good vibes with lowest bidder, then by all means go with him! If it’s just a plain matter of being able to afford the higher one or not, talk with him and see if he can help make the difference. If he can’t, it might be a good idea to save a little longer.
Even if you know nothing about construction, trust your instincts when you’re not getting a good feeling.